Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:42 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 2050/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TargetSearch 2.1.0 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: TargetSearch |
Version: 2.1.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TargetSearch_2.1.0.tar.gz |
StartedAt: 2023-04-12 09:51:14 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 09:52:28 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 73.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TargetSearch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TargetSearch_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TargetSearch.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘TargetSearch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TargetSearch’ version ‘2.1.0’ * 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’ * 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 R 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 8.394 0.328 8.734 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘RICorrection.Rnw’... OK ‘TargetSearch.Rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/TargetSearch.Rcheck/00check.log’ for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rinit.c -o Rinit.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c baseline.c -o baseline.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c detection.c -o detection.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c file.c -o file.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c find_peaks.c -o find_peaks.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c getLine.c -o getLine.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hpf.c -o hpf.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matrix.c -o matrix.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ncdf.c -o ncdf.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c peak.c -o peak.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find_peaks.o getLine.o hpf.o matrix.o ncdf.o peak.o utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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") + } Loading required package: TargetSearchData test_file.R................... 0 tests test_file.R................... 0 tests test_file.R................... 0 tests test_file.R................... 0 tests test_file.R................... 1 tests [0;32mOK[0m test_file.R................... 1 tests [0;32mOK[0m test_file.R................... 1 tests [0;32mOK[0m test_file.R................... 2 tests [0;32mOK[0m test_file.R................... 2 tests [0;32mOK[0m test_file.R................... 3 tests [0;32mOK[0m test_file.R................... 3 tests [0;32mOK[0m test_file.R................... 3 tests [0;32mOK[0m test_file.R................... 4 tests [0;32mOK[0m [0;34m0.1s[0m test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 0 tests test_ncdf4_plot_peak.R........ 5 tests [0;32mOK[0m test_ncdf4_plot_peak.R........ 6 tests [0;32mOK[0m test_ncdf4_plot_peak.R........ 7 tests [0;32mOK[0m test_ncdf4_plot_peak.R........ 7 tests [0;32mOK[0m [0;34m0.3s[0m test_quantMatrix.R............ 0 tests test_quantMatrix.R............ 0 tests test_quantMatrix.R............ 0 tests test_quantMatrix.R............ 0 tests test_quantMatrix.R............ 0 tests test_quantMatrix.R............ 0 tests test_quantMatrix.R............ 1 tests [0;32mOK[0m test_quantMatrix.R............ 2 tests [0;32mOK[0m test_quantMatrix.R............ 2 tests [0;32mOK[0m test_quantMatrix.R............ 2 tests [0;32mOK[0m test_quantMatrix.R............ 3 tests [0;32mOK[0m test_quantMatrix.R............ 4 tests [0;32mOK[0m test_quantMatrix.R............ 4 tests [0;32mOK[0m test_quantMatrix.R............ 4 tests [0;32mOK[0m test_quantMatrix.R............ 5 tests [0;32mOK[0m test_quantMatrix.R............ 5 tests [0;32mOK[0m test_quantMatrix.R............ 5 tests [0;32mOK[0m test_quantMatrix.R............ 6 tests [0;32mOK[0m [0;36m76ms[0m test_ri_data_extract.R........ 0 tests test_ri_data_extract.R........ 0 tests test_ri_data_extract.R........ 0 tests test_ri_data_extract.R........ 0 tests test_ri_data_extract.R........ 1 tests [0;32mOK[0m test_ri_data_extract.R........ 1 tests [0;32mOK[0m test_ri_data_extract.R........ 1 tests [0;32mOK[0m test_ri_data_extract.R........ 2 tests [0;32mOK[0m test_ri_data_extract.R........ 2 tests [0;32mOK[0m test_ri_data_extract.R........ 2 tests [0;32mOK[0m test_ri_data_extract.R........ 3 tests [0;32mOK[0m test_ri_data_extract.R........ 3 tests [0;32mOK[0m test_ri_data_extract.R........ 4 tests [0;32mOK[0m test_ri_data_extract.R........ 4 tests [0;32mOK[0m test_ri_data_extract.R........ 4 tests [0;32mOK[0m test_ri_data_extract.R........ 4 tests [0;32mOK[0m test_ri_data_extract.R........ 4 tests [0;32mOK[0m test_ri_data_extract.R........ 4 tests [0;32mOK[0m test_ri_data_extract.R........ 5 tests [0;32mOK[0m test_ri_data_extract.R........ 5 tests [0;32mOK[0m test_ri_data_extract.R........ 6 tests [0;32mOK[0m [0;34m0.3s[0m test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 0 tests test_ri_plot_peak.R........... 10 tests [0;32mOK[0m test_ri_plot_peak.R........... 11 tests [0;32mOK[0m test_ri_plot_peak.R........... 12 tests [0;32mOK[0m test_ri_plot_peak.R........... 12 tests [0;32mOK[0m [0;36m75ms[0m test_tsLib.R.................. 0 tests test_tsLib.R.................. 0 tests test_tsLib.R.................. 0 tests test_tsLib.R.................. 0 tests test_tsLib.R.................. 0 tests test_tsLib.R.................. 0 tests test_tsLib.R.................. 0 tests test_tsLib.R.................. 1 tests [0;32mOK[0m test_tsLib.R.................. 2 tests [0;32mOK[0m test_tsLib.R.................. 2 tests [0;32mOK[0m test_tsLib.R.................. 2 tests [0;32mOK[0m test_tsLib.R.................. 3 tests [0;32mOK[0m test_tsLib.R.................. 4 tests [0;32mOK[0m test_tsLib.R.................. 4 tests [0;32mOK[0m test_tsLib.R.................. 5 tests [0;32mOK[0m test_tsLib.R.................. 6 tests [0;32mOK[0m test_tsLib.R.................. 7 tests [0;32mOK[0m test_tsLib.R.................. 8 tests [0;32mOK[0m test_tsLib.R.................. 9 tests [0;32mOK[0m test_tsLib.R.................. 10 tests [0;32mOK[0m test_tsLib.R.................. 11 tests [0;32mOK[0m test_tsLib.R.................. 12 tests [0;32mOK[0m [0;36m53ms[0m test_tsRim.R.................. 0 tests test_tsRim.R.................. 1 tests [0;32mOK[0m test_tsRim.R.................. 2 tests [0;32mOK[0m test_tsRim.R.................. 2 tests [0;32mOK[0m test_tsRim.R.................. 3 tests [0;32mOK[0m test_tsRim.R.................. 4 tests [0;32mOK[0m test_tsRim.R.................. 4 tests [0;32mOK[0m test_tsRim.R.................. 5 tests [0;32mOK[0m test_tsRim.R.................. 6 tests [0;32mOK[0m [0;36m4ms[0m test_tsSample.R............... 0 tests test_tsSample.R............... 0 tests test_tsSample.R............... 0 tests test_tsSample.R............... 1 tests [0;32mOK[0m test_tsSample.R............... 2 tests [0;32mOK[0m test_tsSample.R............... 3 tests [0;32mOK[0m test_tsSample.R............... 3 tests [0;32mOK[0m test_tsSample.R............... 3 tests [0;32mOK[0m test_tsSample.R............... 3 tests [0;32mOK[0m test_tsSample.R............... 4 tests [0;32mOK[0m test_tsSample.R............... 5 tests [0;32mOK[0m test_tsSample.R............... 6 tests [0;32mOK[0m test_tsSample.R............... 6 tests [0;32mOK[0m test_tsSample.R............... 7 tests [0;32mOK[0m test_tsSample.R............... 8 tests [0;32mOK[0m test_tsSample.R............... 9 tests [0;32mOK[0m [0;36m32ms[0m All ok, 62 results (1.0s) > > proc.time() user system elapsed 1.190 0.078 1.297
TargetSearch.Rcheck/TargetSearch-Ex.timings
name | user | system | elapsed | |
FAMEoutliers | 0.032 | 0.007 | 0.040 | |
FindAllPeaks | 0.366 | 0.016 | 0.387 | |
FindPeaks | 0.104 | 0.000 | 0.105 | |
ImportFameSettings | 0.010 | 0.001 | 0.011 | |
ImportLibrary | 0.022 | 0.000 | 0.022 | |
ImportSamples | 0.01 | 0.00 | 0.01 | |
NetCDFPeakFinding | 0.105 | 0.031 | 0.137 | |
Profile | 0.543 | 0.004 | 0.547 | |
ProfileCleanUp | 0.407 | 0.008 | 0.414 | |
RIcorrect | 8.394 | 0.328 | 8.734 | |
TSExample | 1.678 | 0.032 | 1.710 | |
Write.Results | 0.051 | 0.000 | 0.051 | |
baseline | 0.234 | 0.000 | 0.235 | |
baselineCorrection | 0.297 | 0.004 | 0.301 | |
baselineCorrectionQuant | 0.416 | 0.008 | 0.425 | |
checkRimLim | 0.607 | 0.052 | 0.659 | |
file | 0.062 | 0.000 | 0.063 | |
fixRI | 0.728 | 0.012 | 0.741 | |
medianRILib | 0.205 | 0.000 | 0.205 | |
ncdf4Convert-method | 0.066 | 0.000 | 0.066 | |
ncdf4_convert | 0.021 | 0.000 | 0.020 | |
ncdf4_convert_from_path | 1.567 | 0.060 | 1.627 | |
ncdf4_data_extract | 0.278 | 0.008 | 0.285 | |
ncdf4_plot_peak | 0.788 | 0.028 | 0.817 | |
ncdf4_update_ri | 0.215 | 0.004 | 0.219 | |
peakCDFextraction | 0.327 | 0.132 | 0.459 | |
peakFind | 0.111 | 0.013 | 0.125 | |
plotFAME | 0.001 | 0.008 | 0.009 | |
plotPeak | 0.121 | 0.010 | 0.131 | |
plotPeakRI | 0.273 | 0.032 | 0.304 | |
plotPeakSimple | 0.205 | 0.016 | 0.222 | |
plotRIdev | 0.242 | 0.008 | 0.250 | |
plotSpectra | 0.12 | 0.00 | 0.12 | |
quantMatrix | 0.351 | 0.016 | 0.366 | |
ri2rt | 0.008 | 0.000 | 0.007 | |
riMatrix | 0.536 | 0.032 | 0.568 | |
ri_data_extract | 0.025 | 0.000 | 0.025 | |
ri_plot_peak | 0.545 | 0.027 | 0.572 | |
rt2ri | 0.003 | 0.000 | 0.003 | |
sampleRI | 0.204 | 0.004 | 0.208 | |
tsLib-class | 0.023 | 0.000 | 0.022 | |
tsMSdata-class | 0.005 | 0.008 | 0.012 | |
tsProfile-class | 0.008 | 0.000 | 0.008 | |
tsRim-class | 0.002 | 0.000 | 0.003 | |
tsSample-class | 0.019 | 0.000 | 0.018 | |
tsUpdate-method | 0.001 | 0.000 | 0.000 | |
updateRI | 0.913 | 0.028 | 0.941 | |
writeLibText | 0.019 | 0.000 | 0.019 | |
writeMSP | 0.013 | 0.000 | 0.014 | |