| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-28 12:04 -0400 (Tue, 28 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 2186/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 2.11.1 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 2.11.1 |
| 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_2.11.1.tar.gz |
| StartedAt: 2025-10-28 01:17:55 -0400 (Tue, 28 Oct 2025) |
| EndedAt: 2025-10-28 01:19:35 -0400 (Tue, 28 Oct 2025) |
| EllapsedTime: 99.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
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###
### 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_2.11.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.11.1’
* 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: ‘MacOSX11.3.1.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 12.55 2.378 15.141
* 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-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘TargetSearch’ ... ** this is package ‘TargetSearch’ version ‘2.11.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.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 installing to /Library/Frameworks/R.framework/Versions/4.5-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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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
FAMEs were saved in /tmp/RtmpmJPY5g/fileb2512522064b.pdf
FAMEs were saved in /tmp/RtmpmJPY5g/fileb2512522064b.pdf
FAMEs were saved in /tmp/RtmpmJPY5g/fileb2512522064b.pdf
FAMEs were saved in /tmp/RtmpmJPY5g/fileb2512522064b.pdf
test_fameoutliers.R........... 5 tests OK 96ms
test_file.R................... 4 tests OK 0.1s
test_import_fame.R............ 14 tests OK 25ms
test_import_library.R......... 15 tests OK 0.1s
test_ncdf4_plot_peak.R........ 7 tests OK 0.4s
test_quantMatrix.R............ 8 tests OK 36ms
test_ri_data_extract.R........ 6 tests OK 5.0s
test_ri_plot_peak.R........... 22 tests OK 0.2s
test_ricorrect.R.............. 5 tests OK 0.5s
test_tsLib.R.................. 30 tests OK 0.1s
test_tsProfile.R.............. 12 tests OK 15ms
test_tsRim.R.................. 9 tests OK 6ms
test_tsSample.R............... 19 tests OK 58ms
test_write_ri_file.R.......... 6 tests OK 13ms
All ok, 181 results (8.5s)
>
> proc.time()
user system elapsed
8.282 0.421 8.919
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.077 | 0.017 | 0.096 | |
| FindAllPeaks | 1.337 | 0.066 | 1.427 | |
| FindPeaks | 0.219 | 0.009 | 0.231 | |
| ImportFameSettings | 0.010 | 0.001 | 0.012 | |
| ImportLibrary | 0.025 | 0.002 | 0.028 | |
| ImportSamples | 0.010 | 0.001 | 0.012 | |
| NetCDFPeakFinding | 0.243 | 0.030 | 0.277 | |
| Profile | 0.904 | 0.028 | 0.936 | |
| ProfileCleanUp | 0.830 | 0.026 | 0.863 | |
| RIcorrect | 12.550 | 2.378 | 15.141 | |
| TSExample | 1.768 | 0.300 | 2.089 | |
| Write.Results | 0.055 | 0.011 | 0.067 | |
| baseline | 0.291 | 0.018 | 0.310 | |
| baselineCorrection | 0.323 | 0.022 | 0.348 | |
| baselineCorrectionQuant | 0.375 | 0.028 | 0.404 | |
| checkRimLim | 1.186 | 0.079 | 1.272 | |
| file | 0.089 | 0.014 | 0.103 | |
| fixRI | 1.224 | 0.097 | 1.329 | |
| makeIndex | 0.003 | 0.002 | 0.005 | |
| medianRILib | 0.482 | 0.023 | 0.509 | |
| ncdf4Convert-method | 0.087 | 0.017 | 0.104 | |
| ncdf4_convert | 0.024 | 0.002 | 0.026 | |
| ncdf4_convert_from_path | 2.554 | 1.021 | 3.668 | |
| ncdf4_data_extract | 0.426 | 0.240 | 0.702 | |
| ncdf4_plot_peak | 1.187 | 0.435 | 1.645 | |
| ncdf4_update_ri | 0.312 | 0.051 | 0.366 | |
| peakCDFextraction | 0.559 | 0.067 | 0.630 | |
| peakFind | 0.246 | 0.017 | 0.264 | |
| plotFAME | 0.007 | 0.003 | 0.012 | |
| plotPeak | 0.249 | 0.020 | 0.271 | |
| plotPeakRI | 0.943 | 0.048 | 1.002 | |
| plotPeakSimple | 0.476 | 0.043 | 0.530 | |
| plotRIdev | 0.411 | 0.028 | 0.441 | |
| plotRefSpectra | 0.091 | 0.007 | 0.099 | |
| plotSpectra | 0.261 | 0.017 | 0.280 | |
| quantMatrix | 0.822 | 0.041 | 0.869 | |
| ri2rt | 0.004 | 0.000 | 0.005 | |
| riMatrix | 1.068 | 0.068 | 1.142 | |
| ri_data_extract | 0.052 | 0.004 | 0.055 | |
| ri_plot_peak | 1.397 | 0.070 | 1.487 | |
| rt2ri | 0.003 | 0.001 | 0.003 | |
| sampleRI | 0.477 | 0.031 | 0.512 | |
| tsLib-class | 0.020 | 0.002 | 0.022 | |
| tsMSdata-class | 0.01 | 0.02 | 0.03 | |
| tsProfile-class | 0.006 | 0.003 | 0.009 | |
| tsRim-class | 0.002 | 0.001 | 0.002 | |
| tsSample-class | 0.017 | 0.002 | 0.019 | |
| tsUpdate-method | 0.001 | 0.000 | 0.000 | |
| updateRI | 0.947 | 0.115 | 1.071 | |
| writeLibText | 0.027 | 0.001 | 0.029 | |
| writeMSP | 0.017 | 0.003 | 0.020 | |