| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 2072/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 2.2.0 (landing page) Alvaro Cuadros-Inostroza
| kjohnson2 | macOS 12.6.1 Monterey / 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: 2.2.0 |
| 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_2.2.0.tar.gz |
| StartedAt: 2023-10-19 06:08:54 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 06:11:54 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 180.2 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_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TargetSearch.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.2.0’
* 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 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 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 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 16.154 1.185 30.591
ncdf4_convert_from_path 3.653 0.384 7.239
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-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/4.3-arm64/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 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_peaks.c -o find_peaks.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 utils.c -o utils.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find_peaks.o get_line.o hpf.o matrix.o ncdf.o peak.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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;34m0.4s[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;34m0.7s[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;36m92ms[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;34m1.2s[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;34m0.2s[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;34m0.1s[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;36m6ms[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;36m73ms[0m
All ok, 62 results (2.7s)
>
> proc.time()
user system elapsed
1.789 0.186 3.559
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.039 | 0.009 | 0.087 | |
| FindAllPeaks | 1.504 | 0.075 | 2.737 | |
| FindPeaks | 0.388 | 0.015 | 0.711 | |
| ImportFameSettings | 0.013 | 0.002 | 0.023 | |
| ImportLibrary | 0.029 | 0.002 | 0.049 | |
| ImportSamples | 0.013 | 0.002 | 0.019 | |
| NetCDFPeakFinding | 0.371 | 0.041 | 0.890 | |
| Profile | 1.418 | 0.047 | 2.569 | |
| ProfileCleanUp | 1.269 | 0.045 | 2.338 | |
| RIcorrect | 16.154 | 1.185 | 30.591 | |
| TSExample | 1.751 | 0.179 | 3.399 | |
| Write.Results | 0.063 | 0.009 | 0.135 | |
| baseline | 0.463 | 0.025 | 0.838 | |
| baselineCorrection | 0.483 | 0.022 | 0.909 | |
| baselineCorrectionQuant | 0.528 | 0.021 | 0.986 | |
| checkRimLim | 1.849 | 0.087 | 3.436 | |
| file | 0.122 | 0.013 | 0.240 | |
| fixRI | 1.744 | 0.085 | 3.206 | |
| medianRILib | 0.775 | 0.029 | 1.424 | |
| ncdf4Convert-method | 0.086 | 0.010 | 0.171 | |
| ncdf4_convert | 0.026 | 0.002 | 0.056 | |
| ncdf4_convert_from_path | 3.653 | 0.384 | 7.239 | |
| ncdf4_data_extract | 0.571 | 0.042 | 1.090 | |
| ncdf4_plot_peak | 1.652 | 0.140 | 3.173 | |
| ncdf4_update_ri | 0.479 | 0.032 | 0.884 | |
| peakCDFextraction | 0.889 | 0.057 | 1.660 | |
| peakFind | 0.402 | 0.025 | 0.775 | |
| plotFAME | 0.009 | 0.005 | 0.022 | |
| plotPeak | 0.375 | 0.018 | 0.687 | |
| plotPeakRI | 1.151 | 0.048 | 2.146 | |
| plotPeakSimple | 0.709 | 0.031 | 1.322 | |
| plotRIdev | 0.553 | 0.031 | 1.057 | |
| plotSpectra | 0.404 | 0.018 | 0.752 | |
| quantMatrix | 1.246 | 0.041 | 2.309 | |
| ri2rt | 0.004 | 0.000 | 0.007 | |
| riMatrix | 1.559 | 0.069 | 2.905 | |
| ri_data_extract | 0.083 | 0.005 | 0.160 | |
| ri_plot_peak | 2.276 | 0.094 | 4.197 | |
| rt2ri | 0.003 | 0.000 | 0.004 | |
| sampleRI | 0.793 | 0.030 | 1.464 | |
| tsLib-class | 0.022 | 0.003 | 0.045 | |
| tsMSdata-class | 0.009 | 0.021 | 0.053 | |
| tsProfile-class | 0.009 | 0.003 | 0.021 | |
| tsRim-class | 0.003 | 0.000 | 0.004 | |
| tsSample-class | 0.034 | 0.004 | 0.069 | |
| tsUpdate-method | 0.000 | 0.001 | 0.000 | |
| updateRI | 1.019 | 0.111 | 2.012 | |
| writeLibText | 0.027 | 0.002 | 0.049 | |
| writeMSP | 0.020 | 0.005 | 0.048 | |