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This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2163/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 2.10.0  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: RELEASE_3_21
git_last_commit: 1a62936
git_last_commit_date: 2025-04-15 09:44:46 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for TargetSearch on merida1

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: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2025-08-19 12:25:08 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 12:28:07 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 178.6 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_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TargetSearch.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘2.10.0’
* 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 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               20.898  3.009  26.000
ncdf4_convert_from_path  4.364  1.365   6.198
* 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-3.21-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 ‘2.10.0’
** 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 RC (2025-06-05 r88288) -- "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  3.9s
FAMEs were saved in /tmp/RtmpnK5VE1/file9e1f3924223b.pdf
FAMEs were saved in /tmp/RtmpnK5VE1/file9e1f3924223b.pdf
FAMEs were saved in /tmp/RtmpnK5VE1/file9e1f3924223b.pdf
FAMEs were saved in /tmp/RtmpnK5VE1/file9e1f3924223b.pdf

test_fameoutliers.R...........    5 tests OK  0.2s

test_file.R...................    4 tests OK  0.2s

test_import_fame.R............   14 tests OK  37ms

test_import_library.R.........   15 tests OK  0.2s

test_ncdf4_plot_peak.R........    7 tests OK  0.8s

test_quantMatrix.R............    8 tests OK  77ms

test_ri_data_extract.R........    6 tests OK  10.3s

test_ri_plot_peak.R...........   22 tests OK  0.3s

test_tsLib.R..................   30 tests OK  0.2s

test_tsProfile.R..............   12 tests OK  37ms

test_tsRim.R..................    9 tests OK  28ms

test_tsSample.R...............   19 tests OK  87ms

test_write_ri_file.R..........    6 tests OK  18ms
All ok, 176 results (16.5s)
> 
> proc.time()
   user  system elapsed 
 14.724   0.566  17.182 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.1250.0220.173
FindAllPeaks2.2120.0892.446
FindPeaks0.3970.0140.437
ImportFameSettings0.0160.0020.020
ImportLibrary0.0460.0040.053
ImportSamples0.0200.0030.025
NetCDFPeakFinding0.4380.0740.568
Profile1.6550.0411.794
ProfileCleanUp1.4280.0391.596
RIcorrect20.898 3.00926.000
TSExample2.9750.3693.716
Write.Results0.1260.0150.165
baseline0.5660.0390.692
baselineCorrection0.5960.0290.691
baselineCorrectionQuant0.6270.0450.717
checkRimLim2.1280.1272.424
file0.1580.0250.188
fixRI2.0490.1202.315
makeIndex0.0060.0040.010
medianRILib0.7990.0360.880
ncdf4Convert-method0.1740.0190.209
ncdf4_convert0.0500.0050.060
ncdf4_convert_from_path4.3641.3656.198
ncdf4_data_extract0.7380.1580.938
ncdf4_plot_peak2.1100.4722.613
ncdf4_update_ri0.5870.2240.822
peakCDFextraction0.9910.1851.189
peakFind0.4950.0430.546
plotFAME0.0140.0060.020
plotPeak0.4300.0230.459
plotPeakRI1.5090.0671.626
plotPeakSimple0.8140.0530.910
plotRIdev0.7500.0330.833
plotRefSpectra0.2040.0080.221
plotSpectra0.4220.0220.466
quantMatrix1.4130.0641.544
ri2rt0.0070.0010.009
riMatrix1.8120.0982.006
ri_data_extract0.0840.0070.096
ri_plot_peak2.2480.1032.474
rt2ri0.0070.0000.009
sampleRI0.8580.0510.956
tsLib-class0.0530.0060.061
tsMSdata-class0.0250.0600.090
tsProfile-class0.0170.0080.026
tsRim-class0.0050.0020.006
tsSample-class0.0430.0060.051
tsUpdate-method000
updateRI1.6460.1531.956
writeLibText0.0410.0020.043
writeMSP0.0390.0070.050