Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 2070/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TargetSearch 2.7.0 (landing page) Alvaro Cuadros-Inostroza
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the TargetSearch package: - 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: 2.7.0 |
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_2.7.0.tar.gz |
StartedAt: 2024-05-20 04:51:22 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 04:52:56 -0400 (Mon, 20 May 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_2.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/TargetSearch.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TargetSearch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TargetSearch’ version ‘2.7.0’ * 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * 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 13.926 1.693 15.926 * 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-mac-arm64/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-arm64/Resources/library’ * installing *source* package ‘TargetSearch’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rinit.c -o Rinit.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c baseline.c -o baseline.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c detection.c -o detection.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file.c -o file.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find.c -o find.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c get_line.c -o get_line.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hpf.c -o hpf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix.c -o matrix.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ncdf.c -o ncdf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c peak.c -o peak.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spectrum.c -o spectrum.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c strutils.c -o strutils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 1.7s test_file.R................... 4 tests OK 0.1s test_import_fame.R............ 14 tests OK 15ms 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 40ms test_ri_data_extract.R........ 6 tests OK 4.8s 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 5ms test_tsSample.R............... 9 tests OK 9ms test_write_ri_file.R.......... 6 tests OK 11ms All ok, 145 results (7.5s) > > proc.time() user system elapsed 7.618 0.285 7.931
TargetSearch.Rcheck/TargetSearch-Ex.timings
name | user | system | elapsed | |
FAMEoutliers | 0.071 | 0.011 | 0.082 | |
FindAllPeaks | 1.350 | 0.050 | 1.442 | |
FindPeaks | 0.232 | 0.008 | 0.241 | |
ImportFameSettings | 0.013 | 0.002 | 0.015 | |
ImportLibrary | 0.024 | 0.001 | 0.025 | |
ImportSamples | 0.011 | 0.002 | 0.013 | |
NetCDFPeakFinding | 0.279 | 0.028 | 0.312 | |
Profile | 0.892 | 0.032 | 0.945 | |
ProfileCleanUp | 0.790 | 0.024 | 0.821 | |
RIcorrect | 13.926 | 1.693 | 15.926 | |
TSExample | 1.996 | 0.266 | 2.277 | |
Write.Results | 0.067 | 0.014 | 0.080 | |
baseline | 0.381 | 0.029 | 0.412 | |
baselineCorrection | 0.395 | 0.020 | 0.418 | |
baselineCorrectionQuant | 0.549 | 0.022 | 0.573 | |
checkRimLim | 1.424 | 0.101 | 1.532 | |
file | 0.097 | 0.014 | 0.113 | |
fixRI | 1.303 | 0.106 | 1.413 | |
medianRILib | 0.474 | 0.019 | 0.494 | |
ncdf4Convert-method | 0.074 | 0.009 | 0.083 | |
ncdf4_convert | 0.021 | 0.002 | 0.022 | |
ncdf4_convert_from_path | 3.047 | 0.516 | 3.634 | |
ncdf4_data_extract | 0.499 | 0.072 | 0.575 | |
ncdf4_plot_peak | 1.457 | 0.166 | 1.628 | |
ncdf4_update_ri | 0.393 | 0.034 | 0.431 | |
peakCDFextraction | 0.675 | 0.079 | 0.757 | |
peakFind | 0.245 | 0.010 | 0.257 | |
plotFAME | 0.009 | 0.007 | 0.016 | |
plotPeak | 0.279 | 0.021 | 0.301 | |
plotPeakRI | 0.933 | 0.043 | 0.986 | |
plotPeakSimple | 0.527 | 0.038 | 0.570 | |
plotRIdev | 0.382 | 0.026 | 0.410 | |
plotRefSpectra | 0.092 | 0.008 | 0.101 | |
plotSpectra | 0.249 | 0.015 | 0.265 | |
quantMatrix | 0.780 | 0.020 | 0.806 | |
ri2rt | 0.003 | 0.000 | 0.003 | |
riMatrix | 1.194 | 0.090 | 1.287 | |
ri_data_extract | 0.052 | 0.004 | 0.067 | |
ri_plot_peak | 1.370 | 0.065 | 1.441 | |
rt2ri | 0.004 | 0.000 | 0.004 | |
sampleRI | 0.488 | 0.020 | 0.513 | |
tsLib-class | 0.021 | 0.005 | 0.025 | |
tsMSdata-class | 0.011 | 0.016 | 0.028 | |
tsProfile-class | 0.009 | 0.004 | 0.012 | |
tsRim-class | 0.002 | 0.001 | 0.003 | |
tsSample-class | 0.020 | 0.002 | 0.022 | |
tsUpdate-method | 0 | 0 | 0 | |
updateRI | 1.024 | 0.129 | 1.160 | |
writeLibText | 0.022 | 0.002 | 0.024 | |
writeMSP | 0.020 | 0.004 | 0.027 | |