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This page was generated on 2025-08-04 12:06 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 2138/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 2.11.0  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: devel
git_last_commit: cf38c16
git_last_commit_date: 2025-07-29 06:07:10 -0400 (Tue, 29 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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 nebbiolo2

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: 2.11.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TargetSearch_2.11.0.tar.gz
StartedAt: 2025-08-04 03:33:39 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 03:35:00 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 81.2 seconds
RetCode: 0
Status:   OK  
CheckDir: TargetSearch.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings TargetSearch_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.11.0’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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 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 8.331   0.53   8.948
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.


Installation output

TargetSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL TargetSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘TargetSearch’ ...
** this is package ‘TargetSearch’ version ‘2.11.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Rinit.c -o Rinit.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c baseline.c -o baseline.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c detection.c -o detection.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c file.c -o file.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c find.c -o find.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c get_line.c -o get_line.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c hpf.c -o hpf.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c matrix.c -o matrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ncdf.c -o ncdf.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c peak.c -o peak.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c spectrum.c -o spectrum.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c strutils.c -o strutils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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-pc-linux-gnu

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  0.8s
FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf
FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf
FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf
FAMEs were saved in /tmp/RtmphX2fFn/file20e76856042cdf.pdf

test_fameoutliers.R...........    5 tests OK  58ms

test_file.R...................    4 tests OK  56ms

test_import_fame.R............   14 tests OK  50ms

test_import_library.R.........   15 tests OK  87ms

test_ncdf4_plot_peak.R........    7 tests OK  0.3s

test_quantMatrix.R............    8 tests OK  27ms

test_ri_data_extract.R........    6 tests OK  3.4s

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

test_ricorrect.R..............    5 tests OK  0.6s

test_tsLib.R..................   30 tests OK  94ms

test_tsProfile.R..............   12 tests OK  16ms

test_tsRim.R..................    9 tests OK  4ms

test_tsSample.R...............   19 tests OK  29ms

test_write_ri_file.R..........    6 tests OK  30ms
All ok, 181 results (6.0s)
> 
> proc.time()
   user  system elapsed 
  5.883   0.132   6.238 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.0550.0070.063
FindAllPeaks0.5740.0070.585
FindPeaks0.1010.0020.104
ImportFameSettings0.0070.0000.007
ImportLibrary0.0160.0010.017
ImportSamples0.0090.0000.009
NetCDFPeakFinding0.1180.0340.157
Profile0.4730.0020.474
ProfileCleanUp0.3860.0040.391
RIcorrect8.3310.5308.948
TSExample1.7920.0971.889
Write.Results0.0480.0020.050
baseline0.2190.0100.229
baselineCorrection0.2140.0100.224
baselineCorrectionQuant0.3010.0100.311
checkRimLim0.6330.0910.724
file0.0550.0040.060
fixRI0.6680.0590.727
makeIndex0.0030.0000.004
medianRILib0.2150.0040.220
ncdf4Convert-method0.0870.0210.108
ncdf4_convert0.0330.0080.042
ncdf4_convert_from_path1.6310.1681.799
ncdf4_data_extract0.3080.0200.328
ncdf4_plot_peak0.8360.0780.914
ncdf4_update_ri0.2170.0120.229
peakCDFextraction0.3620.0460.411
peakFind0.1170.0030.121
plotFAME0.0070.0010.007
plotPeak0.1320.0060.138
plotPeakRI0.4210.0060.427
plotPeakSimple0.2430.0170.259
plotRIdev0.2530.0030.257
plotRefSpectra0.0870.0000.087
plotSpectra0.1220.0020.124
quantMatrix0.4030.0050.408
ri2rt0.0040.0000.004
riMatrix0.5840.0700.654
ri_data_extract0.0270.0010.028
ri_plot_peak0.6150.0120.627
rt2ri0.0040.0000.003
sampleRI0.2360.0020.237
tsLib-class0.0260.0000.027
tsMSdata-class0.0070.0020.010
tsProfile-class0.0070.0010.008
tsRim-class0.0010.0010.002
tsSample-class0.0200.0010.020
tsUpdate-method000
updateRI0.9950.0581.052
writeLibText0.0250.0000.026
writeMSP0.0120.0020.014