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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 79/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anota2seq 1.31.0  (landing page)
Christian Oertlin , Ola Larsson
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/anota2seq
git_branch: devel
git_last_commit: 701f6de
git_last_commit_date: 2025-04-15 11:15:05 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for anota2seq on nebbiolo2

To the developers/maintainers of the anota2seq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/anota2seq.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.

raw results


Summary

Package: anota2seq
Version: 1.31.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:anota2seq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings anota2seq_1.31.0.tar.gz
StartedAt: 2025-09-19 20:59:52 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 21:05:55 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 363.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: anota2seq.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:anota2seq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings anota2seq_1.31.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/anota2seq.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘anota2seq/DESCRIPTION’ ... OK
* this is package ‘anota2seq’ version ‘1.31.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘anota2seq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
anota2seqGetResidOutlierTest 31.631  0.164  31.797
anota2seqGetQualityControl   30.895  0.216  31.114
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
  ...
--- re-building ‘anota2seq.Rnw’ using knitr
Error: processing vignette 'anota2seq.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'anota2seq.tex' failed.
LaTeX errors:
! Package pdftex.def Error: File `figure/badSim.pdf' not found: using draft set
ting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.301 \includegraphics[]{figure/badSim.pdf}
                                           
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘anota2seq.Rnw’

SUMMARY: processing the following file failed:
  ‘anota2seq.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/anota2seq.Rcheck/00check.log’
for details.


Installation output

anota2seq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL anota2seq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘anota2seq’ ...
** this is package ‘anota2seq’ version ‘1.31.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (anota2seq)

Tests output


Example timings

anota2seq.Rcheck/anota2seq-Ex.timings

nameusersystemelapsed
anota2seq-plots000
anota2seqAnalyze0.8090.0130.813
anota2seqDataSetFromMatrix0.0470.0160.063
anota2seqGetContrasts0.4430.0040.442
anota2seqGetCovariates0.4610.0020.464
anota2seqGetDeltaData0.4860.0000.487
anota2seqGetNormalizedData0.0240.0000.024
anota2seqGetOutput0.4120.0000.411
anota2seqGetQualityControl30.895 0.21631.114
anota2seqGetResidOutlierTest31.631 0.16431.797
anota2seqGetThresholds0.4230.0030.426
anota2seqPerformQC000
anota2seqRegModes1.1530.0111.165
anota2seqResidOutlierTest000
anota2seqRun1.3020.0021.305
anota2seqSelSigGenes0.4320.0020.434
anota2seq_data0.0100.0000.009
show-Anota2seqDataSet-method0.0760.0110.087