| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:07 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 2142/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TargetSearch 2.11.1 (landing page) Alvaro Cuadros-Inostroza
| nebbiolo2 | Linux (Ubuntu 24.04.2 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 13.7.1 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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TargetSearch.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings TargetSearch_2.11.1.tar.gz |
| StartedAt: 2025-08-09 07:33:04 -0400 (Sat, 09 Aug 2025) |
| EndedAt: 2025-08-09 07:35:09 -0400 (Sat, 09 Aug 2025) |
| EllapsedTime: 124.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TargetSearch.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings TargetSearch_2.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'TargetSearch' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/TargetSearch/libs/x64/TargetSearch.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 10.03 2.97 19.8
* 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
'F:/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck/00check.log'
for details.
TargetSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL TargetSearch ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'TargetSearch' ... ** this is package 'TargetSearch' version '2.11.1' ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c baseline.c -o baseline.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c detection.c -o detection.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c file.c -o file.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c find.c -o find.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c get_line.c -o get_line.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c hpf.c -o hpf.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c matrix.c -o matrix.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ncdf.c -o ncdf.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c peak.c -o peak.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c spectrum.c -o spectrum.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c strutils.c -o strutils.o gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -shared -s -static-libgcc -o TargetSearch.dll tmp.def 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 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-TargetSearch/00new/TargetSearch/libs/x64 ** 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 ** 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 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 3.9s
FAMEs were saved in F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpsxrAqE\file7998486715c.pdf
FAMEs were saved in F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpsxrAqE\file7998486715c.pdf
FAMEs were saved in F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpsxrAqE\file7998486715c.pdf
FAMEs were saved in F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpsxrAqE\file7998486715c.pdf
test_fameoutliers.R........... 5 tests OK 0.2s
test_file.R................... 4 tests OK 0.1s
test_import_fame.R............ 14 tests OK 64ms
test_import_library.R......... 15 tests OK 0.2s
test_ncdf4_plot_peak.R........ 7 tests OK 0.5s
test_quantMatrix.R............ 8 tests OK 43ms
test_ri_data_extract.R........ 6 tests OK 6.2s
test_ri_plot_peak.R........... 22 tests OK 0.2s
test_ricorrect.R.............. 5 tests OK 0.7s
test_tsLib.R.................. 30 tests OK 0.1s
test_tsProfile.R.............. 12 tests OK 21ms
test_tsRim.R.................. 9 tests OK 7ms
test_tsSample.R............... 19 tests OK 59ms
test_write_ri_file.R.......... 6 tests OK 33ms
All ok, 181 results (12.4s)
>
> proc.time()
user system elapsed
10.50 0.51 12.75
TargetSearch.Rcheck/TargetSearch-Ex.timings
| name | user | system | elapsed | |
| FAMEoutliers | 0.09 | 0.03 | 0.12 | |
| FindAllPeaks | 1.73 | 0.09 | 2.80 | |
| FindPeaks | 0.31 | 0.04 | 0.34 | |
| ImportFameSettings | 0.01 | 0.00 | 0.03 | |
| ImportLibrary | 0.03 | 0.01 | 0.06 | |
| ImportSamples | 0.02 | 0.00 | 0.04 | |
| NetCDFPeakFinding | 0.20 | 0.03 | 0.26 | |
| Profile | 1.03 | 0.03 | 1.06 | |
| ProfileCleanUp | 0.97 | 0.05 | 1.02 | |
| RIcorrect | 10.03 | 2.97 | 19.80 | |
| TSExample | 2.27 | 0.64 | 2.90 | |
| Write.Results | 0.11 | 0.00 | 0.11 | |
| baseline | 0.27 | 0.06 | 0.33 | |
| baselineCorrection | 0.27 | 0.08 | 0.34 | |
| baselineCorrectionQuant | 0.40 | 0.05 | 0.45 | |
| checkRimLim | 0.72 | 0.17 | 0.89 | |
| file | 0.12 | 0.00 | 0.14 | |
| fixRI | 0.89 | 0.17 | 1.07 | |
| makeIndex | 0 | 0 | 0 | |
| medianRILib | 0.63 | 0.02 | 0.64 | |
| ncdf4Convert-method | 0.09 | 0.04 | 0.14 | |
| ncdf4_convert | 0.03 | 0.02 | 0.05 | |
| ncdf4_convert_from_path | 1.68 | 0.48 | 2.19 | |
| ncdf4_data_extract | 0.36 | 0.08 | 0.45 | |
| ncdf4_plot_peak | 1.02 | 0.17 | 1.18 | |
| ncdf4_update_ri | 0.26 | 0.05 | 0.33 | |
| peakCDFextraction | 0.41 | 0.11 | 0.86 | |
| peakFind | 0.37 | 0.02 | 0.39 | |
| plotFAME | 0.00 | 0.01 | 0.02 | |
| plotPeak | 0.10 | 0.08 | 0.17 | |
| plotPeakRI | 1.27 | 0.01 | 1.28 | |
| plotPeakSimple | 0.28 | 0.10 | 0.37 | |
| plotRIdev | 0.58 | 0.03 | 0.61 | |
| plotRefSpectra | 0.11 | 0.00 | 0.11 | |
| plotSpectra | 0.29 | 0.05 | 0.34 | |
| quantMatrix | 1.00 | 0.01 | 1.02 | |
| ri2rt | 0 | 0 | 0 | |
| riMatrix | 0.71 | 0.19 | 0.89 | |
| ri_data_extract | 0.06 | 0.00 | 0.06 | |
| ri_plot_peak | 1.61 | 0.08 | 1.74 | |
| rt2ri | 0 | 0 | 0 | |
| sampleRI | 0.72 | 0.04 | 0.92 | |
| tsLib-class | 0.03 | 0.00 | 0.08 | |
| tsMSdata-class | 0.03 | 0.02 | 0.04 | |
| tsProfile-class | 0.02 | 0.00 | 0.02 | |
| tsRim-class | 0.01 | 0.00 | 0.02 | |
| tsSample-class | 0.02 | 0.02 | 0.04 | |
| tsUpdate-method | 0 | 0 | 0 | |
| updateRI | 1.33 | 0.43 | 1.80 | |
| writeLibText | 0 | 0 | 0 | |
| writeMSP | 0.04 | 0.00 | 0.05 | |