CRAN Package Check Results for Package oncomsm

Last updated on 2024-07-18 07:50:54 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.4 235.08 425.34 660.42 NOTE
r-devel-linux-x86_64-debian-gcc 0.1.4 179.57 328.81 508.38 NOTE
r-devel-linux-x86_64-fedora-clang 0.1.4 845.55 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.4 815.84 NOTE
r-devel-windows-x86_64 0.1.4 173.00 356.00 529.00 NOTE
r-patched-linux-x86_64 0.1.4 153.70 436.15 589.85 NOTE
r-release-linux-x86_64 0.1.4 156.11 426.59 582.70 NOTE
r-release-macos-arm64 0.1.4 191.00 NOTE
r-release-macos-x86_64 0.1.4 274.00 NOTE
r-release-windows-x86_64 0.1.4 185.00 360.00 545.00 NOTE
r-oldrel-macos-arm64 0.1.4 196.00 NOTE
r-oldrel-macos-x86_64 0.1.4 342.00 ERROR
r-oldrel-windows-x86_64 0.1.4 227.00 443.00 670.00 NOTE

Check Details

Version: 0.1.4
Check: for GNU extensions in Makefiles
Result: NOTE GNU make is a SystemRequirements. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 0.1.4
Check: installed package size
Result: NOTE installed size is 49.0Mb sub-directories of 1Mb or more: doc 1.1Mb libs 46.8Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.1.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘avoiding-bias.Rmd’ using rmarkdown Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed. 2023-07-10 21:36:22.865 R[8426:2287719072] XType: Using static font registry. Warning in file.info(x, extra_cols = FALSE) : expanded path length 3828 would be too long for <pre><code class="language-r">library(dplyr) #&gt; #&gt; Attaching package: 'dplyr' #&gt; The following objects are masked from 'package:stats': #&gt; #&gt; filter, lag #&gt; The following objects are masked from 'package:base': #&gt; #&gt; intersect, setdiff, setequal, union library(tidyr) library(oncomsm) </code></pre> <p><strong>tl;dr:</strong> <em>During interim looks, individuals might still be stable and thus ‘at risk’ of either progression or response. Especially when the respective follow-up times differ, or if there is a difference in median time to response and median time to progression, this might lead to bias in the analysis of the response probability.</em></p> <pre><code class="language-r">mdl &lt;- create_srpmodel( A = define_srp_prior( median_t_q05 = c(1, 4, 12), # shorter time to response than progression median_t_q95 = c(6, 8, 36), # essentially fixed shape: shape_q05 = c(0.99, 0.99, 0.9 [... truncated] --- finished re-building ‘avoiding-bias.Rmd’ --- re-building ‘oncomsm.Rmd’ using rmarkdown Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed. Quitting from lines 52-58 [msm-1] (oncomsm.Rmd) Error: processing vignette 'oncomsm.Rmd' failed with diagnostics: Failed to start chrome. Error: --- failed re-building ‘oncomsm.Rmd’ --- re-building ‘prior-choice.Rmd’ using rmarkdown Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed. 2023-07-10 21:36:41.319 R[17427:2287737071] XType: Using static font registry. Warning in file.info(x, extra_cols = FALSE) : expanded path length 9231 would be too long for <pre><code class="language-r">library(dplyr) #&gt; #&gt; Attaching package: 'dplyr' #&gt; The following objects are masked from 'package:stats': #&gt; #&gt; filter, lag #&gt; The following objects are masked from 'package:base': #&gt; #&gt; intersect, setdiff, setequal, union library(tidyr) library(ggplot2) library(oncomsm) </code></pre> <p><strong>tl;dr:</strong> <em>Identification of the shape parameter is difficult settings with little data and it is thus recommended to restrict the shape parameter to \(1\) (exponential model) if no historical data for the construction of an informative prior is available. A beta-mixture prior is suggested for the response probability and log-normal priors on shape and median time-to-next-event for the time-to-event components.</em></p> <h2 id="why-weibull-transition-times">Why Weibull transition times?</h2> <p>In <code>oncomsm</code>, the distributions of the between-state transition times [... truncated] --- finished re-building ‘prior-choice.Rmd’ SUMMARY: processing the following file failed: ‘oncomsm.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-macos-x86_64