Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-28 11:35:17 -0400 (Tue, 28 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4752 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4517 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1661/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qvalue 2.36.0 (landing page) John D. Storey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the qvalue package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qvalue.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: qvalue |
Version: 2.36.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data qvalue |
StartedAt: 2024-05-27 18:47:52 -0400 (Mon, 27 May 2024) |
EndedAt: 2024-05-27 18:48:01 -0400 (Mon, 27 May 2024) |
EllapsedTime: 9.0 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data qvalue ### ############################################################################## ############################################################################## * checking for file ‘qvalue/DESCRIPTION’ ... OK * preparing ‘qvalue’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘qvalue.Rnw’ using knitr Information on package 'qvalue' Description: Package: qvalue Type: Package Title: Q-value estimation for false discovery rate control Version: 2.36.0 Date: 2015-03-24 Authors@R: as.person(c( "John D. Storey <jdstorey@princeton.edu> [aut, cre]", "Andrew J. Bass <ajbass@emory.edu> [aut]", "Alan Dabney [aut]", "David Robinson [aut]", "Gregory Warnes [ctb]" )) Maintainer: John D. Storey <jstorey@princeton.edu>, Andrew J. Bass <ajbass@emory.edu> biocViews: MultipleComparisons Description: This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. VignetteBuilder: knitr Imports: splines, ggplot2, grid, reshape2 Suggests: knitr Depends: R(>= 2.10) URL: http://github.com/jdstorey/qvalue License: LGPL RoxygenNote: 5.0.1 git_url: https://git.bioconductor.org/packages/qvalue git_branch: RELEASE_3_19 git_last_commit: 2cd25e8 git_last_commit_date: 2024-04-30 Repository: Bioconductor 3.19 Date/Publication: 2024-05-27 Author: John D. Storey [aut, cre], Andrew J. Bass [aut], Alan Dabney [aut], David Robinson [aut], Gregory Warnes [ctb] Built: R 4.4.0; ; 2024-05-27 22:47:52 UTC; unix Index: empPvals Calculate p-values from a set of observed test statistics and simulated null test statistics hedenfalk P-values and test-statistics from the Hedenfalk et al. (2001) gene expression dataset hist.qvalue Histogram of p-values lfdr Estimate local False Discovery Rate (FDR) pi0est Proportion of true null p-values plot.qvalue Plotting function for q-value object qvalue Estimate the q-values for a given set of p-values summary.qvalue Display q-value object write.qvalue Write results to file Further information is available in the following vignettes in directory '/tmp/RtmpGIFYMX/Rinst24c8867d9007b6/qvalue/doc': qvalue: qvalue Package (source, pdf) Warning: 'mode(width)' differs between new and previous ==> NOT changing 'width' Warning: 'mode(width)' differs between new and previous ==> NOT changing 'width' Warning: 'mode(width)' differs between new and previous ==> NOT changing 'width' Warning: 'mode(width)' differs between new and previous ==> NOT changing 'width' Error: processing vignette 'qvalue.Rnw' failed with diagnostics: Running 'texi2dvi' on 'qvalue.tex' failed. LaTeX errors: ! Undefined control sequence. l.111 \hlkwd{citation}\hldef {(}\hlsng{"qvalue"}\hldef{)} ? ! Emergency stop. ! Emergency stop. l.111 \hlkwd{citation}\hldef {(}\hlsng{"qvalue"}\hldef{)} End of file on the terminal! ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘qvalue.Rnw’ SUMMARY: processing the following file failed: ‘qvalue.Rnw’ Error: Vignette re-building failed. Execution halted