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This page was generated on 2025-08-30 12:08 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 2145/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 2.11.1  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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 kjohnson3

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: 2025-08-29 22:04:11 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 22:04:44 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 33.5 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 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.11.1’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* 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 4.558  0.429   5.014
* 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-arm64/Resources/library’
* installing *source* package ‘TargetSearch’ ...
** this is package ‘TargetSearch’ version ‘2.11.1’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c find.c -o find.o
clang -arch arm64 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -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 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c spectrum.c -o spectrum.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c strutils.c -o strutils.o
clang -arch arm64 -std=gnu2x -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 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-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)

Tests output

TargetSearch.Rcheck/tests/tinytest.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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  0.6s
FAMEs were saved in /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwFQbwE/fileede346d94616.pdf
FAMEs were saved in /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwFQbwE/fileede346d94616.pdf
FAMEs were saved in /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwFQbwE/fileede346d94616.pdf
FAMEs were saved in /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpwFQbwE/fileede346d94616.pdf

test_fameoutliers.R...........    5 tests OK  27ms

test_file.R...................    4 tests OK  34ms

test_import_fame.R............   14 tests OK  6ms

test_import_library.R.........   15 tests OK  33ms

test_ncdf4_plot_peak.R........    7 tests OK  0.1s

test_quantMatrix.R............    8 tests OK  10ms

test_ri_data_extract.R........    6 tests OK  1.6s

test_ri_plot_peak.R...........   22 tests OK  49ms

test_ricorrect.R..............    5 tests OK  0.2s

test_tsLib.R..................   30 tests OK  30ms

test_tsProfile.R..............   12 tests OK  5ms

test_tsRim.R..................    9 tests OK  1ms

test_tsSample.R...............   19 tests OK  18ms

test_write_ri_file.R..........    6 tests OK  3ms
All ok, 181 results (2.7s)
> 
> proc.time()
   user  system elapsed 
  2.653   0.103   2.785 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.0240.0040.027
FindAllPeaks0.4350.0160.456
FindPeaks0.0780.0050.083
ImportFameSettings0.0030.0010.004
ImportLibrary0.0070.0010.009
ImportSamples0.0030.0010.005
NetCDFPeakFinding0.0910.0100.104
Profile0.2820.0080.301
ProfileCleanUp0.2550.0090.264
RIcorrect4.5580.4295.014
TSExample0.6280.0890.725
Write.Results0.0190.0020.021
baseline0.1190.0070.126
baselineCorrection0.1240.0060.130
baselineCorrectionQuant0.1860.0060.192
checkRimLim0.4270.0240.451
file0.0310.0040.034
fixRI0.4360.0310.469
makeIndex0.0010.0010.002
medianRILib0.1500.0070.156
ncdf4Convert-method0.0250.0060.031
ncdf4_convert0.0070.0010.007
ncdf4_convert_from_path0.9600.1931.174
ncdf4_data_extract0.1590.0140.173
ncdf4_plot_peak0.4260.0460.472
ncdf4_update_ri0.1250.0120.136
peakCDFextraction0.2160.0260.243
peakFind0.0790.0040.089
plotFAME0.0030.0020.005
plotPeak0.0890.0080.098
plotPeakRI0.2960.0140.311
plotPeakSimple0.1660.0180.183
plotRIdev0.1220.0060.129
plotRefSpectra0.0300.0020.031
plotSpectra0.0830.0030.086
quantMatrix0.2510.0080.260
ri2rt0.0010.0000.001
riMatrix0.3750.0310.413
ri_data_extract0.0160.0010.017
ri_plot_peak0.4370.0160.454
rt2ri0.0010.0000.001
sampleRI0.1580.0060.164
tsLib-class0.0060.0000.007
tsMSdata-class0.0030.0050.008
tsProfile-class0.0020.0010.003
tsRim-class0.0010.0010.000
tsSample-class0.0070.0010.007
tsUpdate-method000
updateRI0.3280.0450.376
writeLibText0.0080.0010.008
writeMSP0.0050.0010.005