CRAN Package Check Results for Package geno2proteo

Last updated on 2021-07-24 01:50:03 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.3 15.86 152.53 168.39 OK
r-devel-linux-x86_64-debian-gcc 0.0.3 12.28 115.50 127.78 OK
r-devel-linux-x86_64-fedora-clang 0.0.3 207.13 OK
r-devel-linux-x86_64-fedora-gcc 0.0.3 194.05 OK
r-devel-windows-x86_64 0.0.3 15.00 160.00 175.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.0.3 ERROR
r-patched-linux-x86_64 0.0.3 13.52 146.91 160.43 OK
r-patched-solaris-x86 0.0.3 279.30 OK
r-release-linux-x86_64 0.0.3 14.74 143.59 158.33 OK
r-release-macos-arm64 0.0.3 ERROR
r-release-macos-x86_64 0.0.3 OK
r-release-windows-ix86+x86_64 0.0.3 32.00 152.00 184.00 OK
r-oldrel-macos-x86_64 0.0.3 OK
r-oldrel-windows-ix86+x86_64 0.0.3 32.00 165.00 197.00 OK

Check Details

Version: 0.0.3
Check: examples
Result: ERROR
    Running examples in 'geno2proteo-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: generatingCDSaaFile
    > ### Title: Generating a file containing the DNA and AA sequences of all the
    > ### protein coding regions (CDSs) in a genome
    > ### Aliases: generatingCDSaaFile
    >
    > ### ** Examples
    >
    > # the data folder in this package
    > dataFolder = system.file("extdata", package="geno2proteo")
    >
    > geneticCodeFile_line = file.path(dataFolder,
    + "geneticCode_standardTable_lines.txt")
    > gtfFile = file.path(dataFolder,
    + "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
    > DNAfastaFile = file.path(dataFolder,
    + "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
    >
    > outputFolder = tempdir(); # using the current folder as output folder
    > # calling the function.
    > generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line,
    + gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
    Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
    Calls: generatingCDSaaFile -> read.table -> scan
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 0.0.3
Check: tests
Result: ERROR
     Running 'runTests.R'
    Running the tests in 'tests/runTests.R' failed.
    Last 13 lines of output:
     ERROR in test_generatingCDSaaFile: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
     ERROR in test_genomicLocsToWholeDNASequence: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 13 elements
    
     Test files with failing tests
    
     test_functionsInGeno2proteo.R
     test_generatingCDSaaFile
     test_genomicLocsToWholeDNASequence
    
    
     Error in BiocGenerics:::testPackage("geno2proteo") :
     unit tests failed for package geno2proteo
     Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 0.0.3
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in 'geno2proteoIntroduction.Rnw'
     ...
    
    > tmpFolder = tempdir()
    
    > generatingCDSaaFile(geneticCodeFile_line = geneticCodeFile,
    + gtfFile = gtfFile_chr16, DNAfastaFile = DNAfastaFile_chr16,
    + outputFolder = .... [TRUNCATED]
    
     When sourcing 'geno2proteoIntroduction.R':
    Error: line 2 did not have 7 elements
    Execution halted
    
     'geno2proteoIntroduction.Rnw'... failed
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 0.0.3
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
     ...
    --- re-building 'geno2proteoIntroduction.Rnw' using Sweave
    
    Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
     chunk 3 (label = example_generatingCDSaaFile)
    Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
     line 2 did not have 7 elements
    
    --- failed re-building 'geno2proteoIntroduction.Rnw'
    
    SUMMARY: processing the following file failed:
     'geno2proteoIntroduction.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 0.0.3
Check: package dependencies
Result: ERROR
    Package required but not available: ‘GenomicRanges’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-arm64