Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 2091/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TargetSearch 2.7.1 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2.7.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TargetSearch_2.7.1.tar.gz |
StartedAt: 2024-08-26 23:48:43 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 23:50:18 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 94.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TargetSearch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TargetSearch_2.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TargetSearch.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TargetSearch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TargetSearch’ version ‘2.7.1’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * 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 12.328 2.124 14.647 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/TargetSearch.Rcheck/00check.log’ for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rinit.c -o Rinit.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c baseline.c -o baseline.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c detection.c -o detection.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file.c -o file.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find.c -o find.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c get_line.c -o get_line.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hpf.c -o hpf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix.c -o matrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ncdf.c -o ncdf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c peak.c -o peak.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spectrum.c -o spectrum.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c strutils.c -o strutils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 1.8s test_file.R................... 4 tests OK 0.1s test_import_fame.R............ 14 tests OK 19ms test_import_library.R......... 15 tests OK 0.2s test_ncdf4_plot_peak.R........ 7 tests OK 0.4s test_quantMatrix.R............ 8 tests OK 46ms test_ri_data_extract.R........ 6 tests OK 4.7s test_ri_plot_peak.R........... 22 tests OK 0.2s test_tsLib.R.................. 17 tests OK 55ms test_tsProfile.R.............. 12 tests OK 15ms test_tsRim.R.................. 6 tests OK 6ms test_tsSample.R............... 9 tests OK 10ms test_write_ri_file.R.......... 6 tests OK 13ms All ok, 145 results (7.5s) > > proc.time() user system elapsed 7.478 0.347 7.871
TargetSearch.Rcheck/TargetSearch-Ex.timings
name | user | system | elapsed | |
FAMEoutliers | 0.062 | 0.011 | 0.074 | |
FindAllPeaks | 1.348 | 0.062 | 1.428 | |
FindPeaks | 0.231 | 0.009 | 0.242 | |
ImportFameSettings | 0.014 | 0.002 | 0.017 | |
ImportLibrary | 0.022 | 0.002 | 0.024 | |
ImportSamples | 0.014 | 0.002 | 0.017 | |
NetCDFPeakFinding | 0.241 | 0.034 | 0.279 | |
Profile | 0.916 | 0.035 | 0.960 | |
ProfileCleanUp | 0.800 | 0.027 | 0.838 | |
RIcorrect | 12.328 | 2.124 | 14.647 | |
TSExample | 1.671 | 0.240 | 1.931 | |
Write.Results | 0.064 | 0.012 | 0.078 | |
baseline | 0.313 | 0.021 | 0.338 | |
baselineCorrection | 0.330 | 0.020 | 0.356 | |
baselineCorrectionQuant | 0.389 | 0.026 | 0.420 | |
checkRimLim | 1.268 | 0.101 | 1.391 | |
file | 0.100 | 0.014 | 0.116 | |
fixRI | 1.158 | 0.094 | 1.271 | |
medianRILib | 0.470 | 0.024 | 0.500 | |
ncdf4Convert-method | 0.074 | 0.009 | 0.084 | |
ncdf4_convert | 0.021 | 0.002 | 0.023 | |
ncdf4_convert_from_path | 2.529 | 0.739 | 3.322 | |
ncdf4_data_extract | 0.408 | 0.115 | 0.526 | |
ncdf4_plot_peak | 1.244 | 0.323 | 1.581 | |
ncdf4_update_ri | 0.346 | 0.107 | 0.471 | |
peakCDFextraction | 0.572 | 0.098 | 0.676 | |
peakFind | 0.238 | 0.015 | 0.254 | |
plotFAME | 0.007 | 0.004 | 0.013 | |
plotPeak | 0.256 | 0.019 | 0.277 | |
plotPeakRI | 0.952 | 0.049 | 1.017 | |
plotPeakSimple | 0.473 | 0.032 | 0.508 | |
plotRIdev | 0.390 | 0.020 | 0.414 | |
plotRefSpectra | 0.086 | 0.007 | 0.094 | |
plotSpectra | 0.240 | 0.016 | 0.257 | |
quantMatrix | 0.784 | 0.033 | 0.822 | |
ri2rt | 0.004 | 0.001 | 0.004 | |
riMatrix | 1.051 | 0.070 | 1.128 | |
ri_data_extract | 0.048 | 0.004 | 0.052 | |
ri_plot_peak | 1.380 | 0.074 | 1.473 | |
rt2ri | 0.004 | 0.000 | 0.004 | |
sampleRI | 0.482 | 0.024 | 0.511 | |
tsLib-class | 0.027 | 0.006 | 0.036 | |
tsMSdata-class | 0.010 | 0.022 | 0.033 | |
tsProfile-class | 0.009 | 0.004 | 0.012 | |
tsRim-class | 0.003 | 0.001 | 0.003 | |
tsSample-class | 0.020 | 0.003 | 0.022 | |
tsUpdate-method | 0 | 0 | 0 | |
updateRI | 0.887 | 0.116 | 1.014 | |
writeLibText | 0.022 | 0.001 | 0.023 | |
writeMSP | 0.014 | 0.003 | 0.019 | |