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This page was generated on 2025-09-06 12:06 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 2147/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 2.11.1  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: devel
git_last_commit: 5bc4203
git_last_commit_date: 2025-08-04 03:30:34 -0400 (Mon, 04 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for TargetSearch on lconway

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.

raw results


Summary

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: 2025-09-06 00:18:35 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 00:20:19 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 104.5 seconds
RetCode: 0
Status:   OK  
CheckDir: TargetSearch.Rcheck
Warnings: 0

Command output

##############################################################################
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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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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.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 13.147  2.428  16.052
* 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.


Installation output

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.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)

Tests output

TargetSearch.Rcheck/tests/tinytest.Rout


R version 4.5.1 (2025-06-13) -- "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/RtmpBvyu2E/file50e1603953c0.pdf
FAMEs were saved in /tmp/RtmpBvyu2E/file50e1603953c0.pdf
FAMEs were saved in /tmp/RtmpBvyu2E/file50e1603953c0.pdf
FAMEs were saved in /tmp/RtmpBvyu2E/file50e1603953c0.pdf

test_fameoutliers.R...........    5 tests OK  0.1s

test_file.R...................    4 tests OK  99ms

test_import_fame.R............   14 tests OK  20ms

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  30ms

test_ri_data_extract.R........    6 tests OK  4.9s

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  5ms

test_tsSample.R...............   19 tests OK  55ms

test_write_ri_file.R..........    6 tests OK  13ms
All ok, 181 results (8.5s)
> 
> proc.time()
   user  system elapsed 
  8.415   0.442   9.029 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.0780.0150.095
FindAllPeaks1.4800.0701.581
FindPeaks0.2700.0110.284
ImportFameSettings0.0100.0020.012
ImportLibrary0.0270.0020.030
ImportSamples0.0140.0020.017
NetCDFPeakFinding0.2770.0350.321
Profile1.0160.0371.069
ProfileCleanUp0.9150.0340.964
RIcorrect13.147 2.42816.052
TSExample1.8470.3552.288
Write.Results0.0690.0140.093
baseline0.3370.0280.368
baselineCorrection0.3570.0240.384
baselineCorrectionQuant0.4240.0490.524
checkRimLim1.2900.0991.422
file0.1000.0200.132
fixRI1.2310.0881.326
makeIndex0.0040.0020.007
medianRILib0.4810.0260.509
ncdf4Convert-method0.0860.0180.105
ncdf4_convert0.0240.0040.028
ncdf4_convert_from_path2.5671.0543.710
ncdf4_data_extract0.4380.1530.618
ncdf4_plot_peak1.2110.3241.583
ncdf4_update_ri0.3330.0430.378
peakCDFextraction0.6160.1050.751
peakFind0.2540.0280.285
plotFAME0.0080.0060.015
plotPeak0.2710.0190.292
plotPeakRI0.9590.0401.010
plotPeakSimple0.4700.0400.514
plotRIdev0.4050.0280.437
plotRefSpectra0.0920.0070.100
plotSpectra0.2540.0200.277
quantMatrix0.7610.0350.801
ri2rt0.0030.0000.003
riMatrix1.0430.0701.130
ri_data_extract0.0520.0060.061
ri_plot_peak1.2920.0701.378
rt2ri0.0040.0010.004
sampleRI0.4860.0280.517
tsLib-class0.0230.0030.027
tsMSdata-class0.0080.0180.026
tsProfile-class0.0070.0030.011
tsRim-class0.0020.0010.002
tsSample-class0.0210.0030.023
tsUpdate-method000
updateRI0.9200.1231.057
writeLibText0.0260.0020.028
writeMSP0.0170.0040.021