Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:06 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 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 2138/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TargetSearch 2.11.0 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the TargetSearch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TargetSearch.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: TargetSearch |
Version: 2.11.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TargetSearch_2.11.0.tar.gz |
StartedAt: 2025-08-04 03:33:39 -0400 (Mon, 04 Aug 2025) |
EndedAt: 2025-08-04 03:35:00 -0400 (Mon, 04 Aug 2025) |
EllapsedTime: 81.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TargetSearch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TargetSearch_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘TargetSearch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TargetSearch’ version ‘2.11.0’ * 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 ‘TargetSearch’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed RIcorrect 8.331 0.53 8.948 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck/00check.log’ for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘TargetSearch’ ... ** this is package ‘TargetSearch’ version ‘2.11.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Rinit.c -o Rinit.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c baseline.c -o baseline.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c detection.c -o detection.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c file.c -o file.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c find.c -o find.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c get_line.c -o get_line.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c hpf.c -o hpf.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c matrix.c -o matrix.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ncdf.c -o ncdf.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c peak.c -o peak.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c spectrum.c -o spectrum.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c strutils.c -o strutils.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find.o get_line.o hpf.o matrix.o ncdf.o peak.o spectrum.o strutils.o utils.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-TargetSearch/00new/TargetSearch/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TargetSearch)
TargetSearch.Rcheck/tests/tinytest.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if ( requireNamespace("tinytest", quietly=TRUE) && requireNamespace("TargetSearchData", quietly=TRUE)) { + tinytest::test_package("TargetSearch", color=FALSE, verbose=1) + } Loading required package: TargetSearchData test_FindAllPeaks.R........... 19 tests OK 0.8s FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf test_fameoutliers.R........... 5 tests OK 58ms test_file.R................... 4 tests OK 56ms test_import_fame.R............ 14 tests OK 50ms test_import_library.R......... 15 tests OK 87ms test_ncdf4_plot_peak.R........ 7 tests OK 0.3s test_quantMatrix.R............ 8 tests OK 27ms test_ri_data_extract.R........ 6 tests OK 3.4s test_ri_plot_peak.R........... 22 tests OK 0.3s test_ricorrect.R.............. 5 tests OK 0.6s test_tsLib.R.................. 30 tests OK 94ms test_tsProfile.R.............. 12 tests OK 16ms test_tsRim.R.................. 9 tests OK 4ms test_tsSample.R............... 19 tests OK 29ms test_write_ri_file.R.......... 6 tests OK 30ms All ok, 181 results (6.0s) > > proc.time() user system elapsed 5.883 0.132 6.238
TargetSearch.Rcheck/TargetSearch-Ex.timings
name | user | system | elapsed | |
FAMEoutliers | 0.055 | 0.007 | 0.063 | |
FindAllPeaks | 0.574 | 0.007 | 0.585 | |
FindPeaks | 0.101 | 0.002 | 0.104 | |
ImportFameSettings | 0.007 | 0.000 | 0.007 | |
ImportLibrary | 0.016 | 0.001 | 0.017 | |
ImportSamples | 0.009 | 0.000 | 0.009 | |
NetCDFPeakFinding | 0.118 | 0.034 | 0.157 | |
Profile | 0.473 | 0.002 | 0.474 | |
ProfileCleanUp | 0.386 | 0.004 | 0.391 | |
RIcorrect | 8.331 | 0.530 | 8.948 | |
TSExample | 1.792 | 0.097 | 1.889 | |
Write.Results | 0.048 | 0.002 | 0.050 | |
baseline | 0.219 | 0.010 | 0.229 | |
baselineCorrection | 0.214 | 0.010 | 0.224 | |
baselineCorrectionQuant | 0.301 | 0.010 | 0.311 | |
checkRimLim | 0.633 | 0.091 | 0.724 | |
file | 0.055 | 0.004 | 0.060 | |
fixRI | 0.668 | 0.059 | 0.727 | |
makeIndex | 0.003 | 0.000 | 0.004 | |
medianRILib | 0.215 | 0.004 | 0.220 | |
ncdf4Convert-method | 0.087 | 0.021 | 0.108 | |
ncdf4_convert | 0.033 | 0.008 | 0.042 | |
ncdf4_convert_from_path | 1.631 | 0.168 | 1.799 | |
ncdf4_data_extract | 0.308 | 0.020 | 0.328 | |
ncdf4_plot_peak | 0.836 | 0.078 | 0.914 | |
ncdf4_update_ri | 0.217 | 0.012 | 0.229 | |
peakCDFextraction | 0.362 | 0.046 | 0.411 | |
peakFind | 0.117 | 0.003 | 0.121 | |
plotFAME | 0.007 | 0.001 | 0.007 | |
plotPeak | 0.132 | 0.006 | 0.138 | |
plotPeakRI | 0.421 | 0.006 | 0.427 | |
plotPeakSimple | 0.243 | 0.017 | 0.259 | |
plotRIdev | 0.253 | 0.003 | 0.257 | |
plotRefSpectra | 0.087 | 0.000 | 0.087 | |
plotSpectra | 0.122 | 0.002 | 0.124 | |
quantMatrix | 0.403 | 0.005 | 0.408 | |
ri2rt | 0.004 | 0.000 | 0.004 | |
riMatrix | 0.584 | 0.070 | 0.654 | |
ri_data_extract | 0.027 | 0.001 | 0.028 | |
ri_plot_peak | 0.615 | 0.012 | 0.627 | |
rt2ri | 0.004 | 0.000 | 0.003 | |
sampleRI | 0.236 | 0.002 | 0.237 | |
tsLib-class | 0.026 | 0.000 | 0.027 | |
tsMSdata-class | 0.007 | 0.002 | 0.010 | |
tsProfile-class | 0.007 | 0.001 | 0.008 | |
tsRim-class | 0.001 | 0.001 | 0.002 | |
tsSample-class | 0.020 | 0.001 | 0.020 | |
tsUpdate-method | 0 | 0 | 0 | |
updateRI | 0.995 | 0.058 | 1.052 | |
writeLibText | 0.025 | 0.000 | 0.026 | |
writeMSP | 0.012 | 0.002 | 0.014 | |