Last updated on 2019-12-10 01:52:03 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.3 | 27.36 | 180.43 | 207.79 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3.3 | 20.18 | 263.11 | 283.29 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.3 | 443.67 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.3 | 430.31 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.3.3 | 40.00 | 495.00 | 535.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.3.3 | 38.00 | 490.00 | 528.00 | ERROR | |
| r-patched-linux-x86_64 | 1.3.3 | 23.40 | 327.91 | 351.31 | OK | |
| r-patched-solaris-x86 | 1.3.3 | 536.90 | NOTE | |||
| r-release-linux-x86_64 | 1.3.3 | 23.81 | 328.84 | 352.65 | OK | |
| r-release-windows-ix86+x86_64 | 1.3.3 | 44.00 | 431.00 | 475.00 | OK | |
| r-release-osx-x86_64 | 1.3.3 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.3.3 | 29.00 | 454.00 | 483.00 | OK | |
| r-oldrel-osx-x86_64 | 1.3.3 | OK |
Version: 1.3.3
Check: examples
Result: ERROR
Running examples in 'CHNOSZ-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: affinity
> ### Title: Chemical Affinities of Formation Reactions
> ### Aliases: affinity
>
> ### ** Examples
>
> ## Don't show:
> reset()
reset: resetting "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
> ## End(Don't show)## set up a system and calculate
> ## chemical affinities of formation reactions
> basis(c("SiO2", "MgO", "H2O", "O2"), c(-5, -5, 0, 999))
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(c("SiO2", "MgO", "H2O", "O2"), c(-5, -5, 0, 999))
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x1a54f98>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix") :
the condition has length > 1
Calls: basis -> put.basis
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.3
Check: tests
Result: ERROR
Running 'testthat.R' [45s/50s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#10: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#6: test_that("errors come as expected", {
expect_error(affinity(iprotein = 7), "basis species are not defined")
expect_error(affinity(iprotein = NA), "has some NA values")
expect_error(affinity(iprotein = 0), "are not rownumbers")
basis("CHNOS")
expect_error(affinity(), "species have not been defined")
species("CO2")
expect_error(affinity(pe = c(-10, 10), pH = c(0, 14)), "pe.*does not match any basis species")
expect_error(affinity(O2 = c(-80, -60), pH = c(0, 14)), "pH.*does not match any basis species")
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 1. Error: errors come as expected (@test-affinity.R#10) --------------------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#18: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#17: test_that("output gives T and P in user's units", {
basis("CHNOS")
species("5a(H),14b(H)-cholestane")
a.C_bar <- affinity(T = c(0, 100, 10), P = c(10, 1000, 10))
expect_equal(range(a.C_bar$vals[[1]]), c(0, 100))
expect_equal(range(a.C_bar$vals[[2]]), c(10, 1000))
T.units("K")
P.units("MPa")
a.K_MPa <- affinity(T = c(273.15, 373.15, 10), P = c(1, 100,
10))
expect_equal(range(a.K_MPa$vals[[1]]), c(273.15, 373.15))
expect_equal(range(a.K_MPa$vals[[2]]), c(1, 100))
expect_equal(a.C_bar$values, a.K_MPa$values)
T.units("C")
P.units("bar")
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 2. Error: output gives T and P in user's units (@test-affinity.R#18) -------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#36: basis("CHNOSe")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#35: test_that("pe, pH and Eh are correctly handled", {
basis("CHNOSe")
species(c("HS-", "H2S", "SO4-2"))
Eh <- c(-1, 1)
pe <- convert(Eh, "pe", T = convert(100, "K"))
a.Eh <- affinity(Eh = Eh, T = 100)
a.pe <- affinity(pe = pe, T = 100)
expect_equal(a.Eh$values, a.pe$values, check.attributes = FALSE)
expect_equal(c(a.Eh$vars, a.pe$vars), c("Eh", "pe"))
pH <- c(0, 14)
a <- affinity(pH = pH, Eh = Eh)
expect_equal(a$vars, c("pH", "Eh"))
expect_equal(range(a$vals[[1]]), pH)
expect_equal(range(a$vals[[2]]), Eh)
expect_equal(length(a$vals[[2]]), 128)
a129 <- affinity(pH = pH, Eh = c(Eh, 129))
expect_equal(length(a129$vals[[2]]), 129)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 3. Error: pe, pH and Eh are correctly handled (@test-affinity.R#36) --------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOSe")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-affinity.R#77: basis(c("H2", "O2"), "aq")
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-affinity.R#66: test_that("affinity() in 3D returns values consistent with manual calculation",
{
logK.25 <- subcrt(c("H2", "O2", "H2O"), "aq", c(-1, -0.5,
1), T = 25)$out$logK
logK.100 <- subcrt(c("H2", "O2", "H2O"), "aq", c(-1,
-0.5, 1), T = 100)$out$logK
A.2303RT.25.10.10 <- logK.25 - ((-1) * (-10) + (-0.5) *
(-10))
A.2303RT.100.5.10 <- logK.100 - ((-1) * (-5) + (-0.5) *
(-10))
basis(c("H2", "O2"), "aq")
species("H2O")
a.logK <- affinity(T = c(0, 125, 6), H2 = c(-20, 0, 5),
O2 = c(-20, 0, 5), property = "logK")
expect_equal(dim(a.logK$values[[1]]), c(6, 5, 5), check.names = FALSE)
expect_equal(a.logK$values[[1]][2, 3, 3], logK.25)
expect_equal(a.logK$values[[1]][5, 4, 3], logK.100)
a.A <- affinity(T = c(0, 125, 6), H2 = c(-20, 0, 5),
O2 = c(-20, 0, 5))
expect_equal(a.A$values[[1]][2, 3, 3], A.2303RT.25.10.10)
expect_equal(a.A$values[[1]][5, 4, 3], A.2303RT.100.5.10)
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 4. Error: affinity() in 3D returns values consistent with manual calculation
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("H2", "O2"), "aq")
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-affinity.R#108: basis(c("HCO3-", "H2O", "NH3", "HS-", "H2", "H+"), "aq", c(-3,
0, -4, -7, 999, 999))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-affinity.R#95: test_that("'iprotein' gives consistent results on a transect",
{
A.2303RT_ref <- c(-18.72, -27.894, -35.276, -36.657,
-41.888)
T <- c(93.3, 79.4, 67.5, 65.3, 57.1)
pH <- c(7.35, 7.678, 7.933, 7.995, 8.257)
H2 <- -11 + T * 3/40
reset()
basis(c("HCO3-", "H2O", "NH3", "HS-", "H2", "H+"), "aq",
c(-3, 0, -4, -7, 999, 999))
sites <- c("N", "S", "R", "Q", "P")
file <- system.file("extdata/protein/DS11.csv", package = "CHNOSZ")
aa <- read.csv(file, as.is = TRUE)
ip <- add.protein(aa[1:5, ])
add.obigt("OldAA")
a <- affinity(T = T, pH = pH, H2 = H2, iprotein = ip)
pl <- protein.length(ip)
A.2303RT <- t(sapply(a$values, c))/pl
A.2303RT_max <- apply(A.2303RT, 2, max)
expect_equal(A.2303RT_max, A.2303RT_ref, tolerance = 0.001)
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 5. Error: 'iprotein' gives consistent results on a transect (@test-affinity.R
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(...)
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#136: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#128: test_that("affinity() for proteins (with/without 'iprotein') returns same value as in previous package versions",
{
A.2303RT.nonionized <- -3795.297
A.2303RT.ionized <- -3075.222
basis("CHNOS")
ip <- pinfo("CSG_HALJP")
expect_equal(affinity(iprotein = ip)$values[[1]][1],
A.2303RT.nonionized, tolerance = 1e-06)
species("CSG_HALJP")
expect_equal(affinity()$values[[1]][1], A.2303RT.nonionized,
tolerance = 1e-06)
basis("CHNOS+")
expect_equal(affinity(iprotein = ip)$values[[1]][1],
A.2303RT.ionized, tolerance = 1e-06)
species("CSG_HALJP")
expect_equal(affinity()$values[[1]][1], A.2303RT.ionized,
tolerance = 1e-06)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 6. Error: affinity() for proteins (with/without 'iprotein') returns same valu
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#152: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#150: test_that("affinity() for proteins keeps track of pH on 2-D calculations",
{
basis("CHNOS+")
species("LYSC_CHICK")
a1 <- affinity(pH = c(6, 8, 3))
a2 <- affinity(pH = c(6, 8, 3), T = c(0, 75, 4))
expect_equal(as.numeric(a1$values[[1]]), a2$values[[1]][,
2])
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 7. Error: affinity() for proteins keeps track of pH on 2-D calculations (@tes
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#166: basis("CHNOPS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#159: test_that("IS can be constant or variable", {
oldnon <- nonideal("Alberty")
basis("CHNOPS+")
species(c("PO4-3", "HPO4-2", "H2PO4-"))
a0 <- affinity()
a1 <- affinity(IS = 0.14)
a2 <- affinity(IS = c(0, 0.14))
expect_equal(unlist(lapply(a2$values, head, 1)), unlist(a0$values))
expect_equal(unlist(lapply(a2$values, tail, 1)), unlist(a1$values))
nonideal(oldnon)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 8. Error: IS can be constant or variable (@test-affinity.R#166) ------------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOPS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#178: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#176: test_that("argument recall is usable", {
basis("CHNOS")
species(c("CO2", "CH4"))
a0 <- affinity(O2 = c(-80, -60))
a1 <- affinity(O2 = c(-80, -60), T = 100)
a2 <- affinity(a0, T = 100)
a3 <- affinity(a1, T = 25)
expect_identical(a1, a2)
expect_identical(a0$values, a3$values)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 9. Error: argument recall is usable (@test-affinity.R#178) -----------------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-affinity.R#191: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-affinity.R#189: test_that("sout is processed correctly", {
basis("CHNOS+")
species(c("H2S", "CO2", "CH4"))
a0 <- affinity(T = c(0, 100))
sout <- a0$sout
species(1:2, delete = TRUE)
a1 <- affinity(T = c(0, 100))
a2 <- affinity(T = c(0, 100), sout = a0$sout)
expect_equal(a1$values, a2$values)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 10. Error: sout is processed correctly (@test-affinity.R#191) --------------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-basis.R#24: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-basis.R#21: test_that("invalid basis modification requests cause an error",
{
basis(delete = TRUE)
expect_error(mod.basis("CH4", "gas"), "basis is not defined")
b <- basis("CHNOS+")
expect_error(mod.basis("CH4", "gas"), "is not a formula of one of the basis species")
iCH4 <- info("CH4")
expect_error(mod.basis(iCH4, "gas"), "is not a species index of one of the basis species")
expect_error(mod.basis("CO2", "PPM"), "the elements .* in buffer .* are not in the basis")
expect_error(mod.basis("CO2", "liq"), "state .* not found")
expect_equal(basis(), b)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 11. Error: invalid basis modification requests cause an error (@test-basis.R#
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-basis.R#35: basis(c("copper", "chalcocite"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-basis.R#34: test_that("modifying states of basis species is possible", {
b1 <- basis(c("copper", "chalcocite"))
b2 <- basis("Cu2S", "cr2")
expect_equal(sum(b2$ispecies - b1$ispecies), 1)
expect_error(basis("Cu2S", "cr4"), "state or buffer 'cr4' not found for chalcocite")
basis("CHNOS+")
expect_equal(basis("CO2", "gas")$state[1], "gas")
expect_equal(basis("CO2", "aq")$state[1], "aq")
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 12. Error: modifying states of basis species is possible (@test-basis.R#35)
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("copper", "chalcocite"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-diagram.R#5: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-diagram.R#3: test_that("expected errors are produced for inconsistent arguments",
{
expect_error(diagram(list()), "'eout' does not look like output from equil\\(\\) or affinity\\(\\)")
basis("CHNOS")
species(c("glycine", "alanine"))
a <- affinity()
expect_message(diagram(a, plot.it = FALSE), "balance: moles of CO2 in formation reactions")
e <- equilibrate(a)
expect_error(diagram(e, "Z"), "Z is not a valid diagram type")
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 13. Error: expected errors are produced for inconsistent arguments (@test-dia
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-diagram.R#14: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-diagram.R#13: test_that("expected messages, errors and results arise using output from affinity()",
{
basis("CHNOS+")
basis("O2", "CO2-AC")
species(c("formic acid", "formate", "acetic acid", "acetate"))
a <- affinity()
expect_error(diagram(a, "loga.equil"), "'eout' is not the output from equil\\(\\)")
expect_error(diagram(a, "O2"), "is not numeric - was a buffer selected\\?")
expect_message(diagram(a, plot.it = FALSE), "balance: moles of CO2 in formation reactions")
d.1 <- diagram(a, balance = 1, plot.it = FALSE)
d.CO2 <- diagram(a, plot.it = FALSE)
expect_equal(as.numeric(d.CO2$plotvals), as.numeric(d.1$plotvals)/c(1,
1, 2, 2))
basis("O2", -90)
a <- affinity(O2 = c(-80, -70))
expect_error(diagram(a, "CO2", groups = list(1:2, 3:4)),
"can't plot equilibrium activities of basis species for grouped species")
expect_error(diagram(a, "CO2", alpha = TRUE), "equilibrium activities of basis species not available with alpha=TRUE")
d <- diagram(a, "CO2", plot.it = FALSE)
a <- affinity(O2 = d$vals[[1]], CO2 = d$plotvals[[4]])
expect_equal(a$values[[4]], array(numeric(128)))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 14. Error: expected messages, errors and results arise using output from affi
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-diagram.R#44: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-diagram.R#43: test_that("'groups' and 'alpha' work as expected", {
basis("CHNOS+")
species(c("formic acid", "formate", "acetic acid", "acetate"))
a <- affinity(O2 = c(-80, -60))
e <- equilibrate(a)
d <- diagram(e, groups = list(1:2, 3:4), plot.it = FALSE)
n.balance <- balance(a)$n.balance
expect_equal(d$plotvals[[1]], log10(n.balance[1] * 10^e$loga.equil[[1]] +
n.balance[2] * 10^e$loga.equil[[2]]))
expect_equal(d$plotvals[[2]], log10(n.balance[3] * 10^e$loga.equil[[3]] +
n.balance[4] * 10^e$loga.equil[[4]]))
d <- diagram(e, alpha = TRUE, plot.it = FALSE)
expect_equal(Reduce("+", d$plotvals), array(rep(1, 128)),
check.attributes = FALSE)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 15. Error: 'groups' and 'alpha' work as expected (@test-diagram.R#44) ------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-diagram.R#62: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-diagram.R#61: test_that("'normalize' and 'as.residue' work as expected", {
basis("CHNOS")
species(c("LYSC_CHICK", "MYG_PHYCA", "RNAS1_BOVIN", "CYC_BOVIN"))
a <- affinity(O2 = c(-80, -70))
expect_error(diagram(a, normalize = TRUE), "can be TRUE only for a 2-D \\(predominance\\) diagram")
a <- affinity(H2O = c(-10, 0), O2 = c(-80, -70))
d1 <- diagram(a, normalize = TRUE, plot.it = FALSE)
e <- equilibrate(a, normalize = TRUE)
d2 <- diagram(e, plot.it = FALSE)
expect_equal(d1$predominant, d2$predominant)
expect_error(diagram(e, normalize = TRUE), "can be TRUE only if 'eout' is the output from affinity\\(\\)")
d3 <- diagram(a, as.residue = TRUE, plot.it = FALSE)
e <- equilibrate(a, as.residue = TRUE)
d4 <- diagram(e, plot.it = FALSE)
expect_equal(d3$predominant, d4$predominant)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 16. Error: 'normalize' and 'as.residue' work as expected (@test-diagram.R#62)
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-diagram.R#81: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-diagram.R#80: test_that("diagram() handles 2D plots with different x and y resolution and warns for >1 species in contour plot",
{
basis("CHNOS")
species(c("alanine", "glycine", "serine", "methionine"))
a <- affinity(T = c(0, 200, 6), O2 = c(-90, -60, 5))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 17. Error: diagram() handles 2D plots with different x and y resolution and w
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-diagram.R#90: basis(c("H2", "O2", "CO2"), c(-7.19, -60, -2.65))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-diagram.R#88: test_that("NaN values from equilibrate() are preserved (as NA in predominance calculation)",
{
basis(c("H2", "O2", "CO2"), c(-7.19, -60, -2.65))
species(c("n-hexadecanol", "n-hexadecanoic acid", "n-octadecanol",
"n-octadecanoic acid"), c("liq", "liq", "liq", "liq"))
a <- affinity(H2 = c(-12, 0), O2 = c(-90, -50), T = 30)
e <- equilibrate(a, balance = 1)
d <- diagram(e, plot.it = FALSE)
expect_equal(d$predominant[1, 128], as.numeric(NA))
expect_equal(d$predominant[128, 1], as.numeric(NA))
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 18. Error: NaN values from equilibrate() are preserved (as NA in predominance
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("H2", "O2", "CO2"), c(-7.19, -60, -2.65))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-equilibrate.R#5: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(NULL, exprs, env)
where 16: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 17: force(code)
where 18: doWithOneRestart(return(expr), restart)
where 19: withOneRestart(expr, restarts[[1L]])
where 20: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 21: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 22: FUN(X[[i]], ...)
where 23: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 24: force(code)
where 25: doWithOneRestart(return(expr), restart)
where 26: withOneRestart(expr, restarts[[1L]])
where 27: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 28: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 29: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 30: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 31: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 32: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 19. Error: (unknown) (@test-equilibrate.R#5) -------------------------------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-logmolality.R#62: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-logmolality.R#3: test_that("non-zero ionic strength transforms variables from activity to molality",
{
wprop <- water(c("A_DH", "B_DH"), P = 1)
speciesprops <- subcrt(c("H+", "HCO3-", "CO2"), T = 25)$out
nonid <- nonideal(c("H+", "HCO3-", "CO2"), speciesprops,
IS = 1, T = 298.15, P = 1, A_DH = wprop$A_DH, B_DH = wprop$B_DH)
expect_maxdiff(nonid[[2]]$loggam, -0.1868168, 1e-07)
out1 <- subcrt(c("H+", "HCO3-", "CO2"), T = 25, IS = 1)$out
loggam_HCO3 <- out1[[2]]$loggam
loggam_CO2 <- out1[[3]]$loggam
expect_equal(nonid[[2]]$loggam, loggam_HCO3)
expect_equal(nonid[[3]]$loggam, loggam_CO2)
out0 <- subcrt(c("H+", "HCO3-", "CO2"), T = 25)$out
expect_equal(out1[[2]]$G - out0[[2]]$G, -convert(loggam_HCO3,
"G"))
expect_equal(out1[[3]]$G - out0[[3]]$G, -convert(loggam_CO2,
"G"))
logK <- subcrt(c("CO2", "H2O", "H+", "HCO3-"), c(-1,
-1, 1, 1), T = 25)$out$logK
expect_maxdiff(logK, -6.344694, 1e-06)
logQ0 <- (-7 + -3) - (0 + -3)
A0manual <- -convert(logK - logQ0, "G")
A0subcrt <- subcrt(c("CO2", "H2O", "H+", "HCO3-"), c(-1,
-1, 1, 1), T = 25, logact = c(-3, 0, -7, -3))$out$A
expect_equal(A0subcrt, A0manual)
logaHCO3 <- -3 + loggam_HCO3
logaCO2 <- -3 + loggam_CO2
logQ1 <- (-7 + logaHCO3) - (0 + logaCO2)
A1manual <- -convert(logK - logQ1, "G")
A1subcrt <- subcrt(c("CO2", "H2O", "H+", "HCO3-"), c(-1,
-1, 1, 1), T = 25, logact = c(-3, 0, -7, -3), IS = 1)$out$A
expect_equal(A1subcrt, A1manual)
basis("CHNOS+")
species(c("CO2", "HCO3-"))
a0 <- affinity()
A0affinity <- -convert(a0$values[[2]], "G")
expect_equal(A0affinity[[1]], A0subcrt)
a1 <- affinity(IS = 1)
A1affinity <- -convert(a1$values[[2]], "G")
expect_equal(A1affinity[[1]], A1subcrt)
swap.basis("CO2", "HCO3-")
basis("HCO3-", -3)
a0 <- affinity()
a1 <- affinity(IS = 1)
expect_equal(a0$values[[2]][1], 0)
expect_equal(a1$values[[2]][1], 0)
ACO2_0affinity <- -convert(a0$values[[1]], "G")
ACO2_1affinity <- -convert(a1$values[[1]], "G")
logKrev <- -logK
logQrev0 <- -logQ0
logQrev1 <- -logQ1
ACO2_0manual <- -convert(logKrev - logQrev0, "G")
ACO2_1manual <- -convert(logKrev - logQrev1, "G")
expect_equal(ACO2_0manual, ACO2_0affinity[[1]])
expect_equal(ACO2_1manual, ACO2_1affinity[[1]])
e0 <- equilibrate(a0)
e1 <- equilibrate(a1)
logact_HCO3 <- e0$loga.equil[[2]]
logact_CO2 <- e0$loga.equil[[1]]
logQeq0 <- (-7 + logact_HCO3) - (logact_CO2 + 0)
Aeq0 <- -convert(logK - logQeq0, "G")
expect_equal(Aeq0[[1]], 0)
logact_HCO3 <- e1$loga.equil[[2]]
logact_CO2 <- e1$loga.equil[[1]]
logQeq1 <- (-7 + logact_HCO3 + loggam_HCO3) - (logact_CO2 +
loggam_CO2 + 0)
Aeq1 <- -convert(logK - logQeq1, "G")
expect_equal(Aeq1[[1]], 0)
a.balance <- 10^e1$loga.balance
m.total <- sum(10^unlist(e1$loga.equil))
expect_equal(a.balance, m.total)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 20. Error: non-zero ionic strength transforms variables from activity to mola
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-makeup.R#50: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-makeup.R#45: test_that("makeup has a fall-through mechanism for matrices and named objects",
{
expect_equal(makeup(makeup("CH4")), makeup("CH4"))
expect_equal(makeup(list(makeup("CH4"))), list(makeup("CH4")))
basis("CHNOS")
expect_equal(species.basis("CH4")[1, ], species.basis(info("CH4"))[1,
])
expect_equal(species.basis(makeup("CH4"))[1, ], species.basis("CH4")[1,
])
protein <- c("LYSC_CHICK", "RNAS1_BOVIN", "CYC_BOVIN",
"MYG_PHYCA", "MYG_HORSE")
pf <- protein.formula(protein)
basis(protein)
bmat <- basis.elements()
expect_equal(makeup(pf)[[1]], makeup(as.chemical.formula(pf)[1]))
expect_equal(makeup(pf), makeup(bmat))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 21. Error: makeup has a fall-through mechanism for matrices and named objects
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-mosaic.R#4: basis(c("CO2", "H2O", "NH3", "O2"), c(0, 0, 0, 0))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-mosaic.R#3: test_that("results are consistent with affinity()", {
basis(c("CO2", "H2O", "NH3", "O2"), c(0, 0, 0, 0))
species(c("alanine", "glycine"))
a25 <- affinity()
m1_25 <- mosaic("NH3", "CO2")
expect_equal(a25$values, m1_25$A.species$values)
m2_25 <- mosaic("NH3", "CO2", blend = FALSE)
expect_equal(a25$values, m2_25$A.species$values)
a500 <- affinity(T = 500)
m1_500 <- mosaic("NH3", "CO2", T = 500)
expect_equal(a500$values, m1_500$A.species$values)
m2_500 <- mosaic("NH3", "CO2", blend = FALSE, T = 500)
expect_equal(a500$values, m2_500$A.species$values)
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 22. Error: results are consistent with affinity() (@test-mosaic.R#4) -------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("CO2", "H2O", "NH3", "O2"), c(0, 0, 0, 0))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-mosaic.R#29: basis(c("FeO", "SO4-2", "H2O", "H+", "e-"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-mosaic.R#24: test_that("blend=TRUE produces reasonable values", {
basis(c("FeO", "SO4-2", "H2O", "H+", "e-"))
basis("SO4-2", -6)
basis("Eh", -0.15)
species(c("hematite", "magnetite"))
bases <- c("SO4-2", "HSO4-", "HS-", "H2S")
pH <- c(0, 14, 29)
m1 <- mosaic(bases, pH = pH, blend = FALSE)
m2 <- mosaic(bases, pH = pH)
expect_equivalent(m2$A.species$values[[1]], m1$A.species$values[[1]])
species(c("pyrrhotite", "pyrite"))
m3 <- mosaic(bases, pH = pH, blend = FALSE)
m4 <- mosaic(bases, pH = pH)
expect_equal(sapply(m3$A.species$values, "[", 13), sapply(m4$A.species$values,
"[", 13), tol = 0.1)
expect_equal(sapply(m3$A.species$values, "[", 1), sapply(m4$A.species$values,
"[", 1), tol = 1e-07)
expect_equal(sapply(m3$A.species$values, "[", 29), sapply(m4$A.species$values,
"[", 29), tol = 1e-13)
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 23. Error: blend=TRUE produces reasonable values (@test-mosaic.R#29) -------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("FeO", "SO4-2", "H2O", "H+", "e-"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-mosaic.R#55: basis(c("CO2", "NH3", "O2", "H2O", "H+"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-mosaic.R#53: test_that("mosaic() - equilibrate() produces equilibrium activities",
{
basis(c("CO2", "NH3", "O2", "H2O", "H+"))
species(c("acetamide", "acetic acid", "acetate"))
m <- mosaic(c("NH3", "NH4+"), pH = c(0, 14))
e <- equilibrate(m$A.species)
s1 <- subcrt(c("acetic acid", "NH4+", "acetamide", "water",
"H+"), c(-1, -1, 1, 1, 1), T = 25)
logK1 <- s1$out$logK
loga_acetic <- e$loga.equil[[2]]
loga_NH4 <- m$E.bases[[1]]$loga.equil[[2]]
loga_acetamide <- e$loga.equil[[1]]
loga_H2O <- m$E.bases[[1]]$basis$logact[[4]]
loga_Hplus <- -m$E.bases[[1]]$vals$pH
logQ1 <- -loga_acetic - loga_NH4 + loga_acetamide + loga_H2O +
loga_Hplus
A1 <- logQ1 - logK1
expect_equivalent(A1, rep(0, length(A1)))
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 24. Error: mosaic() - equilibrate() produces equilibrium activities (@test-mo
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("CO2", "NH3", "O2", "H2O", "H+"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-mosaic.R#83: basis(c("Au", "Cl-", "H2S", "H2O", "oxygen", "H+"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-mosaic.R#77: test_that("mosaic() - solubility() produces equilibrium activities",
{
T <- 250
P <- 500
basis(c("Au", "Cl-", "H2S", "H2O", "oxygen", "H+"))
species(c("Au(HS)2-", "AuHS", "AuOH", "AuCl2-"))
basis("H2S", -2)
basis("O2", -40)
NaCl <- NaCl(T = T, P = P, m_tot = 1)
basis("Cl-", log10(NaCl$m_Cl))
bases <- c("H2S", "HS-", "HSO4-", "SO4-2")
m <- mosaic(bases, pH = c(2, 10), T = 250, P = 500, IS = NaCl$IS)
s <- solubility(m$A.species)
s1 <- subcrt(c("Au", "H2S", "oxygen", "Au(HS)2-", "H2O",
"H+"), c(-1, -2, -0.25, 1, 0.5, 1), T = T, P = P,
IS = NaCl$IS)
logK1 <- s1$out$logK
loga_Au <- m$A.bases$basis$logact[[1]]
loga_H2S <- m$E.bases[[1]]$loga.equil[[1]]
logf_O2 <- m$A.bases$basis$logact[[5]]
loga_AuHS2minus <- s$loga.equil[[1]]
loga_H2O <- m$A.bases$basis$logact[[4]]
loga_Hplus <- -m$A.bases$vals$pH
logQ1 <- -1 * loga_Au - 2 * loga_H2S - 0.25 * logf_O2 +
1 * loga_AuHS2minus + 0.5 * loga_H2O + 1 * loga_Hplus
A1 <- logQ1 - logK1
expect_equivalent(A1, rep(0, length(A1)))
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 25. Error: mosaic() - solubility() produces equilibrium activities (@test-mos
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("Au", "Cl-", "H2S", "H2O", "oxygen", "H+"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-mosaic.R#122: basis(c("FeO", "SO4-2", "H2O", "H+", "e-", "CO3-2"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-mosaic.R#116: test_that("mosaic() - equilibrate() produces equilibrium activities that are consistent with\n stability differences of minerals and multiple groups of changing basis species",
{
basis(c("FeO", "SO4-2", "H2O", "H+", "e-", "CO3-2"))
basis("SO4-2", -6)
basis("CO3-2", 0)
basis("pH", 6.3)
species(c("pyrrhotite", "pyrite", "hematite", "magnetite",
"siderite"))
bases <- list(c("SO4-2", "HSO4-", "HS-", "H2S"), c("CO3-2",
"HCO3-", "CO2"))
m <- mosaic(bases, Eh = c(-0.5, 0))
s1 <- subcrt(c("pyrite", "CO2", "H2O", "H+", "e-", "siderite",
"H2S"), c(-1, -1, -1, -2, -2, 1, 2), T = 25)
logK <- s1$out$logK
loga_pyrite <- loga_siderite <- loga_H2O <- 0
loga_Hplus <- m$A.bases[[1]]$basis$logact[[4]]
loga_eminus <- -convert(m$A.bases[[1]]$vals$Eh, "pe")
loga_H2S <- m$E.bases[[1]]$loga.equil[[4]]
loga_CO2 <- m$E.bases[[2]]$loga.equil[[3]]
logQ <- -1 * loga_pyrite - 1 * loga_CO2 - 1 * loga_H2O -
2 * loga_Hplus - 2 * loga_eminus + 1 * loga_siderite +
2 * loga_H2S
A <- logQ - logK
Adiff <- A - (m$A.species$values[[2]] - m$A.species$values[[5]])
expect_equivalent(Adiff, rep(0, length(Adiff)))
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 26. Error: mosaic() - equilibrate() produces equilibrium activities that are
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("FeO", "SO4-2", "H2O", "H+", "e-", "CO3-2"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-nonideal.R#54: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-nonideal.R#53: test_that("affinity transect incorporates IS correctly", {
basis("CHNOS+")
species("acetate")
basis("O2", -80)
a80_0 <- affinity()
basis("O2", -60)
a60_1 <- affinity(IS = 1)
a <- affinity(O2 = seq(-80, -60, length.out = 4), IS = seq(0,
1, length.out = 4))
expect_equal(a$values[[1]][1], a80_0$values[[1]][1])
expect_equal(a$values[[1]][4], a60_1$values[[1]][1])
a25_0 <- affinity()
a50_1 <- affinity(T = 50, IS = 1)
a <- affinity(T = seq(25, 50, length.out = 4), IS = seq(0,
1, length.out = 4))
expect_equal(a$values[[1]][1], a25_0$values[[1]][1])
expect_equal(a$values[[1]][4], a50_1$values[[1]][1])
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 27. Error: affinity transect incorporates IS correctly (@test-nonideal.R#54)
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-protein.info.R#19: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-protein.info.R#16: test_that("protein.equil() reports values consistent with Dick and Shock (2011)",
{
protein <- pinfo(c("CSG_METVO", "CSG_METJA"))
suppressMessages(add.obigt("OldAA"))
basis("CHNOS+")
suppressMessages(swap.basis("O2", "H2"))
pequil <- protein.equil(protein, loga.protein = -3)
expect_true(any(grepl(c("0\\.435.*1\\.36"), pequil)))
expect_true(any(grepl(c("-3\\.256.*-2\\.834"), pequil)))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 28. Error: protein.equil() reports values consistent with Dick and Shock (201
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-revisit.R#7: basis("CHNOS")
where 5: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
where 6 at testthat/test-revisit.R#4: suppressMessages({
add.obigt("OldAA")
basis("CHNOS")
basis("O2", -65)
species(c("leucine", "glycine", "glutamic acid"))
a <- affinity()
e0 <- equilibrate(a)
a <- affinity(O2 = c(-75, -65))
e1 <- equilibrate(a)
a <- affinity(O2 = c(-75, -65), NH3 = c(-4, 100, 3))
e2 <- equilibrate(a)
a <- affinity(O2 = c(-75, -65, 4), H2O = c(-8, 0, 3), NH3 = c(-6,
-4, 2))
e3 <- equilibrate(a)
})
where 7: eval(code, test_env)
where 8: eval(code, test_env)
where 9: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 10: doTryCatch(return(expr), name, parentenv, handler)
where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 13: doTryCatch(return(expr), name, parentenv, handler)
where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 15: tryCatchList(expr, classes, parentenv, handlers)
where 16: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 17: test_code(NULL, exprs, env)
where 18: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 19: force(code)
where 20: doWithOneRestart(return(expr), restart)
where 21: withOneRestart(expr, restarts[[1L]])
where 22: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 23: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 24: FUN(X[[i]], ...)
where 25: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 26: force(code)
where 27: doWithOneRestart(return(expr), restart)
where 28: withOneRestart(expr, restarts[[1L]])
where 29: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 30: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 31: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 32: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 33: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 34: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 29. Error: (unknown) (@test-revisit.R#4) -----------------------------------
the condition has length > 1
Backtrace:
1. base::suppressMessages(...)
3. CHNOSZ::basis("CHNOS")
4. CHNOSZ:::preset.basis(species[1])
5. CHNOSZ::basis(species, logact)
6. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-solubility.R#11: basis(c("carbon dioxide", "H2O", "O2", "H+"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-solubility.R#3: test_that("solubility() produces stable conditions (affinity = 0)",
{
pH <- c(0, 14)
res <- 100
T <- 25
IS <- 0
basis(c("carbon dioxide", "H2O", "O2", "H+"))
basis("CO2", -3.5)
species(c("CO2", "HCO3-", "CO3-2"))
a <- affinity(pH = c(pH, res), T = T, IS = IS)
s <- solubility(a)
checkfun <- function(i) {
logact <- sapply(s$loga.equil, "[", i)
species(1:3, logact)
basis("pH", s$vals[[1]][i])
affinity(T = T, IS = IS)
}
expect_equal(max(abs(unlist(checkfun(33)$values))), 0)
expect_equal(max(abs(unlist(checkfun(99)$values))), 0)
basis(c("calcite", "Ca+2", "H2O", "O2", "H+"))
species(c("CO2", "HCO3-", "CO3-2"))
a <- affinity(pH = c(pH, res), T = T, IS = IS)
s <- solubility(a)
checkfun <- function(i) {
logact <- sapply(s$loga.equil, "[", i)
species(1:3, logact)
basis("pH", s$vals[[1]][i])
basis("Ca+2", s$loga.balance[i])
affinity(T = T, IS = IS)
}
expect_equal(max(abs(unlist(checkfun(33)$values))), 0)
expect_equal(max(abs(unlist(checkfun(99)$values))), 0)
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 30. Error: solubility() produces stable conditions (affinity = 0) (@test-solu
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("carbon dioxide", "H2O", "O2", "H+"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-solubility.R#48: basis(c("calcite", "H2O", "Ca+2", "O2", "H+"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-solubility.R#46: test_that("solubility() catches some error conditions", {
basis(c("calcite", "H2O", "Ca+2", "O2", "H+"))
species(c("CO2", "HCO3-", "CO3-2"))
a <- affinity()
expect_message(solubility(a), "test for dissociation reaction returns FALSE")
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 31. Error: solubility() catches some error conditions (@test-solubility.R#48)
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("calcite", "H2O", "Ca+2", "O2", "H+"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-species.R#9: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-species.R#6: test_that("species not contained by basis cause errors", {
expect_error(species("H2O"), "basis species are not defined")
expect_error(species.basis("H2O"), "basis species are not defined")
basis("CHNOS")
expect_error(species.basis("U"), "element\\(s\\) not in the basis\\: U")
expect_error(species("fayalite"), "element\\(s\\) not in the basis\\: Fe Si")
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 32. Error: species not contained by basis cause errors (@test-species.R#9) -
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-species.R#15: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-species.R#14: test_that("for one or more species, species.basis() keeps track of zeroes and puts elements in order of thermo$basis",
{
basis("CHNOS")
test0 <- count.elements("OHN0")
test1 <- count.elements("HN0O")
expect_equal(species.basis(test0), species.basis(test1))
expect_equal(unique(as.numeric(species.basis(makeup(c("C",
"CCN"))))), 0)
expect_equal(species.basis(makeup(c("C", "CCN"), count.zero = TRUE))[2,
, drop = FALSE], species.basis(makeup("CCN")))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 33. Error: for one or more species, species.basis() keeps track of zeroes and
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
-- 34. Error: deleting nonexistent species causes error or warning (@test-specie
basis species are not defined
Backtrace:
1. CHNOSZ::species("H2O")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-species.R#35: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-species.R#34: test_that("non-available species cause error, and species can be added or modified",
{
basis("CHNOS")
expect_error(species("wate"), "species not available")
sdef <- species("CO2")
expect_equal(nrow(species("CO2")), 1)
expect_equal(species(1, "gas")$state, "gas")
expect_equal(species(1, -5)$logact, -5)
expect_equal(nrow(species("CO2")), 2)
expect_equal(nrow(species(info("alanine"))), 3)
expect_equal(species(3)$name, "alanine")
expect_equal(nrow(species("alanine", "cr")), 4)
expect_equal(species("alanine", -7)$logact[3], -7)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 35. Error: non-available species cause error, and species can be added or mod
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-species.R#58: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-species.R#57: test_that("index_return provides indices for touched species",
{
basis("CHNOS")
expect_equal(species("CO2", index.return = TRUE), 1)
expect_equal(species("CO2", index.return = TRUE), 1)
expect_equal(species(c("H2O", "NH3"), index.return = TRUE),
c(2, 3))
expect_equal(species(1, "gas", index.return = TRUE),
1)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 36. Error: index_return provides indices for touched species (@test-species.R
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-subcrt.R#8: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-subcrt.R#6: test_that("unbalanced reactions give a warning or are balanced given sufficient basis species",
{
expect_warning(subcrt(c("glucose", "ethanol"), c(-1,
3)), "reaction was unbalanced, missing H-6O3")
basis("CHNOS")
s <- subcrt(c("malic acid", "citric acid"), c(-1, 1))
expect_equal(s$reaction$coeff, c(-1, 1, -2, -1, 1.5))
expect_equal(s$reaction$name, c("malic acid", "citric acid",
"CO2", "water", "oxygen"))
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 37. Error: unbalanced reactions give a warning or are balanced given sufficie
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-subcrt.R#161: basis(c("copper", "chalcocite"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-subcrt.R#152: test_that("duplicated species yield correct phase transitions",
{
s1 <- subcrt("chalcocite", T = c(100, 1000), P = 1000)
s2 <- subcrt(rep("chalcocite", 2), T = c(100, 1000),
P = 1000)
expect_equal(s1$out[[1]]$logK, s2$out[[1]]$logK)
expect_equal(s1$out[[1]]$logK, s2$out[[2]]$logK)
basis(c("copper", "chalcocite"))
species("chalcocite")
a <- affinity(T = c(0, 1000, 2), P = 1)
expect_equal(as.numeric(a$values[[1]]), c(0, 0))
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 38. Error: duplicated species yield correct phase transitions (@test-subcrt.R
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("copper", "chalcocite"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-swap.basis.R#8: basis("CHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-swap.basis.R#6: test_that("swap.basis raises errors when needed", {
expect_error(swap.basis(c("CO2", "H2O")), "requires an existing basis definition")
basis("CHNOS+")
expect_error(swap.basis(c("CO2", "H2O")), "two species must be identified")
expect_error(swap.basis(c("CO2", "H2O"), c("HCO3-", "H2O")),
"can only swap one species for one species")
expect_error(swap.basis("CH4", "C2H5OH"), "basis species .* is not defined")
expect_error(swap.basis("CO2", "C60"), "is not available")
expect_error(swap.basis("CO2", "H2"), "the number of basis species is greater than the number of elements and charge")
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 39. Error: swap.basis raises errors when needed (@test-swap.basis.R#8) -----
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-swap.basis.R#18: basis(c("graphite", "H2"), c("cr", "gas"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-swap.basis.R#16: test_that("basis.logact only accepts defined elements", {
basis(c("graphite", "H2"), c("cr", "gas"))
expect_error(basis.logact(c(C = 1)), "number of elements in 'emu' is less than those in basis")
ispecies <- info(c("ethane", "propane", "acetic acid", "propanoic acid"))
w <- run.wjd(ispecies, as.chemical.formula(colMeans(i2A(ispecies))))
ep <- equil.potentials(w)
expect_error(basis.logact(ep), "element\\(s\\) O not found in basis")
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 40. Error: basis.logact only accepts defined elements (@test-swap.basis.R#18)
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("graphite", "H2"), c("cr", "gas"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-swap.basis.R#30: basis(c("graphite", "H2", "O2"), c("cr", "gas", "gas"))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-swap.basis.R#29: test_that("equil.potentials - basis.logact - element.mu makes a roundtrip at 25 and 99 degrees C",
{
basis(c("graphite", "H2", "O2"), c("cr", "gas", "gas"))
ispecies <- info(c("ethane", "propane", "acetic acid",
"propanoic acid"))
w25 <- run.wjd(ispecies, as.chemical.formula(colMeans(i2A(ispecies))))
ep25 <- equil.potentials(w25)
bl25 <- basis.logact(ep25)
basis(names(bl25), bl25)
expect_equal(element.mu(), ep25)
w99 <- run.wjd(ispecies, as.chemical.formula(colMeans(i2A(ispecies))),
T = 99)
ep99 <- equil.potentials(w99)
bl99 <- basis.logact(ep99, T = 99)
basis(names(bl99), bl99)
expect_equal(element.mu(T = 99), ep99)
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 41. Error: equil.potentials - basis.logact - element.mu makes a roundtrip at
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("graphite", "H2", "O2"), c("cr", "gas", "gas"))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-swap.basis.R#50: basis("FeCHNOS+")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-swap.basis.R#49: test_that("swapping works with a buffer (no recalculation of activities)",
{
basis("FeCHNOS+")
oldb <- basis("O2", "PPM")
newb <- swap.basis("O2", "hydrogen")
expect_identical(oldb$logact, newb$logact)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 42. Error: swapping works with a buffer (no recalculation of activities) (@te
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("FeCHNOS+")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-util.affinity.R#20: basis("CHNOSe")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-util.affinity.R#14: test_that("A.ionization() handles arguments generated by energy.args()",
{
basis("CHNOSe")
ea <- energy.args(list(CO2 = c(-5, 0, 6), pH = c(0, 14,
2), Eh = c(-1, 0, 3), T = c(25, 28, 4)))
A <- A.ionization(1, ea$vars, ea$vals)
expect_equal(dim(A[[1]]), c(6, 2, 3, 4))
ea <- energy.args(list(pH = c(0, 14, 2), Eh = c(-1, 0,
2)))
A <- A.ionization(1, ea$vars, ea$vals)
expect_equal(dim(A[[1]]), c(2, 2))
A <- A.ionization(1, vars = character(), vals = list())
expect_equal(dim(A[[1]]), 1)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 43. Error: A.ionization() handles arguments generated by energy.args() (@test
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOSe")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-util.affinity.R#36: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-util.affinity.R#34: test_that("energy() includes ionization affinities of proteins when needed",
{
basis("CHNOS")
species(c("alanine", "LYSC_CHICK"))
ea <- energy.args(list(T = c(25, 50, 2), O2 = c(-80,
-60, 3)))
Anonion <- do.call(energy, ea)
basis("CHNOS+")
basis("pH", 11)
species(c("alanine", "LYSC_CHICK"))
ea <- energy.args(list(T = c(25, 50, 2), O2 = c(-80,
-60, 3)))
Aion.pH11 <- do.call(energy, ea)
expect_equal(Anonion$a[[1]], Aion.pH11$a[[1]])
A.ionization.LYSC_CHICK <- Aion.pH11$a[[2]] - Anonion$a[[2]]
A.ionization.2550 <- ionize.aa(pinfo(pinfo("LYSC_CHICK")),
property = "A", T = c(25, 50), pH = 11)
expect_equal(A.ionization.LYSC_CHICK[, 1], A.ionization.2550[,
1], check.attributes = FALSE)
expect_equal(A.ionization.LYSC_CHICK[, 3], A.ionization.2550[,
1], check.attributes = FALSE)
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 44. Error: energy() includes ionization affinities of proteins when needed (@
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-util.program.R#20: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-util.program.R#15: test_that("other functions are calling palply() properly", {
if (min(getOption("mc.cores"), 2) > 1 & parallel::detectCores() >
1) {
basis("CHNOS")
ip <- 1:nrow(thermo()$protein)
expect_message(a <- affinity(iprotein = rep(ip, 3)),
"affinity running .* calculations")
expect_message(e <- equilibrate(a, normalize = TRUE),
"equil.boltzmann running .* calculations")
species(c("CO2", "acetic acid"))
a <- affinity(O2 = c(-90, -60, 1000))
expect_message(e <- equilibrate(a), "equil.reaction running 1000 calculations")
}
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 45. Error: other functions are calling palply() properly (@test-util.program.
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-water.lines.R#20: basis(c("H2O", "H+", "e-"), c(logaH2O[i], -7, -7))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(desc, code, env = parent.frame())
where 14 at testthat/test-water.lines.R#14: test_that("water.lines() masks H2 and O2 fields on diagrams with pH as x-axis",
{
if (plot.it)
par(mfrow = c(3, 6))
Ts <- c(25, 100, 25)
logaH2O <- c(0, 0, -5)
for (i in 1:3) {
T <- Ts[i]
basis(c("H2O", "H+", "e-"), c(logaH2O[i], -7, -7))
species(c("H2O", "O2", "H2"), c("liq", "gas", "gas"))
n1 <- nspecies(affinity(pH = c(-2, 16, res), Eh = c(-1,
1.5, res), T = T))
n2 <- nspecies(affinity(pH = c(-2, 16, res), pe = c(-20,
25, res), T = T))
swap.basis("e-", "oxygen")
n3 <- nspecies(affinity(pH = c(-2, 16, res), O2 = c(-90,
10, res), T = T))
swap.basis("oxygen", "O2")
n4 <- nspecies(affinity(pH = c(-2, 16, res), O2 = c(-90,
10, res), T = T))
swap.basis("O2", "hydrogen")
n5 <- nspecies(affinity(pH = c(-2, 16, res), H2 = c(-50,
10, res), T = T))
swap.basis("hydrogen", "H2")
n6 <- nspecies(affinity(pH = c(-2, 16, res), H2 = c(-50,
10, res), T = T))
expect_equal(c(n1, n2, n3, n4, n5, n6), c(1, 1, 1,
1, 1, 1))
}
})
where 15: eval(code, test_env)
where 16: eval(code, test_env)
where 17: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 21: doTryCatch(return(expr), name, parentenv, handler)
where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 23: tryCatchList(expr, classes, parentenv, handlers)
where 24: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 25: test_code(NULL, exprs, env)
where 26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 27: force(code)
where 28: doWithOneRestart(return(expr), restart)
where 29: withOneRestart(expr, restarts[[1L]])
where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 32: FUN(X[[i]], ...)
where 33: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 34: force(code)
where 35: doWithOneRestart(return(expr), restart)
where 36: withOneRestart(expr, restarts[[1L]])
where 37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 38: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 41: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 46. Error: water.lines() masks H2 and O2 fields on diagrams with pH as x-axis
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("H2O", "H+", "e-"), c(logaH2O[i], -7, -7))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at testthat/test-water.lines.R#43: basis(c("H2O", "H+", "e-"), c(0, -7, -7))
where 3: eval(code, test_env)
where 4: eval(code, test_env)
where 5: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 9: doTryCatch(return(expr), name, parentenv, handler)
where 10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 13: test_code(NULL, exprs, env)
where 14: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 15: force(code)
where 16: doWithOneRestart(return(expr), restart)
where 17: withOneRestart(expr, restarts[[1L]])
where 18: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 19: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 20: FUN(X[[i]], ...)
where 21: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 22: force(code)
where 23: doWithOneRestart(return(expr), restart)
where 24: withOneRestart(expr, restarts[[1L]])
where 25: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 26: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 27: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 28: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 29: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 30: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 47. Error: (unknown) (@test-water.lines.R#43) ------------------------------
the condition has length > 1
Backtrace:
1. CHNOSZ::basis(c("H2O", "H+", "e-"), c(0, -7, -7))
2. CHNOSZ:::put.basis(ispecies, logact)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4 at testthat/test-wjd.R#52: basis("CHNOS")
where 5: eval(code, test_env)
where 6: eval(code, test_env)
where 7: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 11: doTryCatch(return(expr), name, parentenv, handler)
where 12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 13: tryCatchList(expr, classes, parentenv, handlers)
where 14: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 15: test_code(desc, code, env = parent.frame())
where 16 at testthat/test-wjd.R#21: test_that("open-system equilibrium distributions reproduce the results of wjd()",
{
reset()
add.obigt("OldAA")
y <- yeastgfp("lipid.particle")
aa <- yeast.aa(y$protein)
ina <- is.na(y$abundance) | is.na(aa$chains)
aa <- aa[!ina, ]
aa.625 <- aa[, 6:25]
aa[, 6:25] <- aa.625/rowSums(aa.625)
iprotein <- add.protein(aa)
iobigt <- info(paste(aa$protein, aa$organism, sep = "_"))
Y <- rep(100, length(iobigt))
w <- run.wjd(iobigt, Y = Y, Gfrac = 1e-15, nlambda = 501)
X.closed <- w$X
ep <- equil.potentials(w)
basis("CHNOS")
bl <- basis.logact(ep)
basis(names(bl), bl)
a <- affinity(iprotein = iprotein)
e <- equilibrate(a, loga.balance = log10(sum(Y)))
X.open <- 10^unlist(e$loga.equil)
expect_equal(X.closed, X.open, tolerance = 0.018)
reset()
})
where 17: eval(code, test_env)
where 18: eval(code, test_env)
where 19: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 20: doTryCatch(return(expr), name, parentenv, handler)
where 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 27: test_code(NULL, exprs, env)
where 28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
where 29: force(code)
where 30: doWithOneRestart(return(expr), restart)
where 31: withOneRestart(expr, restarts[[1L]])
where 32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 33: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
{
reporter$start_file(basename(path))
lister$start_file(basename(path))
source_file(path, new.env(parent = env), chdir = TRUE,
wrap = wrap)
reporter$.end_context()
reporter$end_file()
})
where 34: FUN(X[[i]], ...)
where 35: lapply(paths, test_file, env = env, reporter = current_reporter,
start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
where 36: force(code)
where 37: doWithOneRestart(return(expr), restart)
where 38: withOneRestart(expr, restarts[[1L]])
where 39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
where 40: with_reporter(reporter = current_reporter, results <- lapply(paths,
test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
load_helpers = FALSE, wrap = wrap))
where 41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 42: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap)
where 43: test_package_dir(package = package, test_path = test_path, filter = filter,
reporter = reporter, ..., stop_on_failure = stop_on_failure,
stop_on_warning = stop_on_warning, wrap = wrap)
where 44: test_check("CHNOSZ")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x4407e60>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
-- 48. Error: open-system equilibrium distributions reproduce the results of wjd
the condition has length > 1
Backtrace:
1. CHNOSZ::basis("CHNOS")
2. CHNOSZ:::preset.basis(species[1])
3. CHNOSZ::basis(species, logact)
4. CHNOSZ:::put.basis(ispecies, logact)
== testthat results ===========================================================
[ OK: 365 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 48 ]
1. Error: errors come as expected (@test-affinity.R#10)
2. Error: output gives T and P in user's units (@test-affinity.R#18)
3. Error: pe, pH and Eh are correctly handled (@test-affinity.R#36)
4. Error: affinity() in 3D returns values consistent with manual calculation (@test-affinity.R#77)
5. Error: 'iprotein' gives consistent results on a transect (@test-affinity.R#108)
6. Error: affinity() for proteins (with/without 'iprotein') returns same value as in previous package versions (@test-affinity.R#136)
7. Error: affinity() for proteins keeps track of pH on 2-D calculations (@test-affinity.R#152)
8. Error: IS can be constant or variable (@test-affinity.R#166)
9. Error: argument recall is usable (@test-affinity.R#178)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.3
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'anintro.Rmd' using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4: basis("CHNOSe")
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: withVisible(eval(expr, envir, enclos))
where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 14: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 20: process_file(text, output)
where 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,
encoding = encoding)
where 22: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
...)
where 23: vweave_rmarkdown(...)
where 24: engine$weave(file, quiet = quiet, encoding = enc)
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 29: tools:::.buildOneVignette("anintro.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "anintro", "UTF-8", "/tmp/RtmprDz9bN/file103e5923b0b1.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x8874090>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 212-216 (anintro.Rmd)
Error: processing vignette 'anintro.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'anintro.Rmd'
--- re-building 'eos-regress.Rmd' using rmarkdown
EOSplot: plotting line for P=279.96 bar
EOSplot: plotting line for P=279.96 bar
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
EOSplot: plotting line for P=279.96 bar
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
checkEOS: Cp of methane aq (841) differs by -2.61 cal K-1 mol-1 from tabulated value
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=1000 bar
EOSplot: plotting line for P=1000 bar
add.obigt: read 3 rows; made 2 replacements, 1 additions [energy units: cal]
add.obigt: use obigt() or reset() to restore default database
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 25 C and 1 bar (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
H O Si
-4 -4 -1
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 50 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
H O Si
-4 -4 -1
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 11 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
H O Si
-4 -4 -1
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
H O Si
-4 -4 -1
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 11 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
H O Si
-4 -4 -1
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 2 species at 11 values of T (C) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
H O Si
-4 -4 -1
info.character: found H4SiO4(aq); other available state is aq
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 3 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
info.character: found H4SiO4(aq); other available state is aq
info.character: found SiO2(aq); other available phases are coesite, cristobalite,alpha, cristobalite,beta, quartz, quartz,beta, tridymite,high, tridymite,low
info.character: found H2O(liq); other available state is cr
subcrt: 3 species at 15 values of T (C) and P (bar) (wet) [energy units: cal]
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(c("Al+3", "H4SiO4", "K+", "H2O", "H+", "O2"))
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 13: block_exec(params)
where 14: call_block(x)
where 15: process_group.block(group)
where 16: process_group(group)
where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 18: process_file(text, output)
where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,
encoding = encoding)
where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
...)
where 21: vweave_rmarkdown(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 27: tools:::.buildOneVignette("eos-regress.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "eos-regress", "UTF-8", "/tmp/RtmprDz9bN/file103e87ba310.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x8a53130>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 435-440 (eos-regress.Rmd)
Error: processing vignette 'eos-regress.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'eos-regress.Rmd'
--- re-building 'obigt.Rmd' using rmarkdown
--- finished re-building 'obigt.Rmd'
--- re-building 'equilibrium.Rnw' using knitr
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2: basis(species, logact)
where 3: preset.basis(species[1])
where 4: basis("CHNOS")
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: withVisible(eval(expr, envir, enclos))
where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 14: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 20: process_file(text, output)
where 21: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",
file)) knit2pandoc else knit)(file, encoding = encoding,
quiet = quiet, envir = globalenv(), ...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 27: tools:::.buildOneVignette("equilibrium.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "equilibrium", "latin-9", "/tmp/RtmprDz9bN/file103e2ae30589.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x2875210>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 225-229 (equilibrium.Rnw)
Error: processing vignette 'equilibrium.Rnw' failed with diagnostics:
the condition has length > 1
--- failed re-building 'equilibrium.Rnw'
--- re-building 'hotspring.Rnw' using knitr
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
CHNOSZ
--- call from context ---
put.basis(ispecies, logact)
--- call from argument ---
if (class(try(solve(comp), silent = TRUE)) == "try-error") stop("singular stoichiometric matrix")
--- R stacktrace ---
where 1: put.basis(ispecies, logact)
where 2 at <text>#2: basis(c("HCO3-", "H2O", "NH3", "HS-", "H2", "H+"))
where 3: setup.basis()
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: withVisible(eval(expr, envir, enclos))
where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 14: block_exec(params)
where 15: call_block(x)
where 16: process_group.block(group)
where 17: process_group(group)
where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 19: process_file(text, output)
where 20: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",
file)) knit2pandoc else knit)(file, encoding = encoding,
quiet = quiet, envir = globalenv(), ...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
}, error = function(e) {
OK <<- FALSE
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::.buildOneVignette("hotspring.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CHNOSZ.Rcheck/vign_test/CHNOSZ",
TRUE, FALSE, "hotspring", "latin-9", "/tmp/RtmprDz9bN/file103e5231dd83.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (ispecies, logact = rep(NA, length(ispecies)))
{
thermo <- get("thermo", CHNOSZ)
state <- thermo$obigt$state[ispecies]
comp <- makeup(ispecies, count.zero = TRUE)
comp <- sapply(comp, c)
comp <- t(comp)
rownames(comp) <- as.character(thermo$obigt$formula[ispecies])
if ("(Z-1)" %in% rownames(comp))
rownames(comp)[rownames(comp) == "(Z-1)"] <- "e-"
if (nrow(comp) > ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is greater than the number of elements and charge")
else stop("the number of basis species is greater than the number of elements")
}
if (nrow(comp) < ncol(comp)) {
if ("Z" %in% colnames(comp))
stop("the number of basis species is less than the number of elements and charge")
else stop("the number of basis species is less than the number of elements")
}
if (class(try(solve(comp), silent = TRUE)) == "try-error")
stop("singular stoichiometric matrix")
comp <- cbind(as.data.frame(comp), ispecies, logact, state,
stringsAsFactors = FALSE)
thermo$basis <- comp
assign("thermo", thermo, CHNOSZ)
species(delete = TRUE)
return(thermo$basis)
}
<bytecode: 0x3cd3778>
<environment: namespace:CHNOSZ>
--- function search by body ---
Function put.basis in namespace CHNOSZ has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 247-250 (hotspring.Rnw)
Error: processing vignette 'hotspring.Rnw' failed with diagnostics:
the condition has length > 1
--- failed re-building 'hotspring.Rnw'
SUMMARY: processing the following files failed:
'anintro.Rmd' 'eos-regress.Rmd' 'equilibrium.Rnw' 'hotspring.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [55s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
── 1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the
c(r0.qqr$H) not equal to tail(r1.qqr$H, 1).
Attributes: < target is NULL, current is list >
── 2. Failure: referenced objectives give expected results (@test-revisit.R#65)
head(r1.spearman$H, 1) not equal to -1.
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 563 | SKIPPED: 0 | WARNINGS: 130 | FAILED: 2 ]
1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the same conditions (@test-revisit.R#40)
2. Failure: referenced objectives give expected results (@test-revisit.R#65)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [85s/118s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
── 1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the
c(r0.qqr$H) not equal to tail(r1.qqr$H, 1).
Attributes: < target is NULL, current is list >
── 2. Failure: referenced objectives give expected results (@test-revisit.R#65)
head(r1.spearman$H, 1) not equal to -1.
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 563 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the same conditions (@test-revisit.R#40)
2. Failure: referenced objectives give expected results (@test-revisit.R#65)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [81s/98s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
── 1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the
c(r0.qqr$H) not equal to tail(r1.qqr$H, 1).
Attributes: < target is NULL, current is list >
── 2. Failure: referenced objectives give expected results (@test-revisit.R#65)
head(r1.spearman$H, 1) not equal to -1.
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 563 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the same conditions (@test-revisit.R#40)
2. Failure: referenced objectives give expected results (@test-revisit.R#65)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.3.3
Check: running tests for arch ‘i386’
Result: ERROR
Running 'testthat.R' [50s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
-- 1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the
c(r0.qqr$H) not equal to tail(r1.qqr$H, 1).
Attributes: < target is NULL, current is list >
-- 2. Failure: referenced objectives give expected results (@test-revisit.R#65)
head(r1.spearman$H, 1) not equal to -1.
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
== testthat results ===========================================================
[ OK: 563 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the same conditions (@test-revisit.R#40)
2. Failure: referenced objectives give expected results (@test-revisit.R#65)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8
Version: 1.3.3
Check: running tests for arch ‘x64’
Result: ERROR
Running 'testthat.R' [59s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(CHNOSZ)
CHNOSZ version 1.3.3 (2019-08-02)
reset: creating "thermo" object
obigt: loading default database with 1849 aqueous, 3372 total species
>
> # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
> # (since we use makeCluster() etc via palply)
> Sys.setenv("R_TESTS" = "")
>
> test_check("CHNOSZ")
-- 1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the
c(r0.qqr$H) not equal to tail(r1.qqr$H, 1).
Attributes: < target is NULL, current is list >
-- 2. Failure: referenced objectives give expected results (@test-revisit.R#65)
head(r1.spearman$H, 1) not equal to -1.
Attributes: < Modes: list, NULL >
Attributes: < Lengths: 1, 0 >
Attributes: < names for target but not for current >
Attributes: < current is not list-like >
== testthat results ===========================================================
[ OK: 563 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
1. Failure: 0-D, 1-D, 2-D and 3-D calculations give identical results at the same conditions (@test-revisit.R#40)
2. Failure: referenced objectives give expected results (@test-revisit.R#65)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8
Version: 1.3.3
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 2.5Mb
Flavor: r-patched-solaris-x86