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This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 2072/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 2.2.0  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: RELEASE_3_17
git_last_commit: 4ab2240
git_last_commit_date: 2023-04-25 09:48:42 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for TargetSearch on kjohnson2


To the developers/maintainers of the TargetSearch package:
- 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: 2.2.0
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_2.2.0.tar.gz
StartedAt: 2023-10-19 06:08:54 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 06:11:54 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 180.2 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_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TargetSearch.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.2.0’
* 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 R 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               16.154  1.185  30.591
ncdf4_convert_from_path  3.653  0.384   7.239
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘TargetSearch’ ...
** 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 arm64 -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 -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 -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 -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c find_peaks.c -o find_peaks.o
clang -arch arm64 -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 -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 -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 -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 -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 -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 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find_peaks.o get_line.o hpf.o matrix.o ncdf.o peak.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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")
+ }
Loading required package: TargetSearchData

test_file.R...................    0 tests    
test_file.R...................    0 tests    
test_file.R...................    0 tests    
test_file.R...................    0 tests    
test_file.R...................    1 tests OK 
test_file.R...................    1 tests OK 
test_file.R...................    1 tests OK 
test_file.R...................    2 tests OK 
test_file.R...................    2 tests OK 
test_file.R...................    3 tests OK 
test_file.R...................    3 tests OK 
test_file.R...................    3 tests OK 
test_file.R...................    4 tests OK 0.4s

test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    0 tests    
test_ncdf4_plot_peak.R........    5 tests OK 
test_ncdf4_plot_peak.R........    6 tests OK 
test_ncdf4_plot_peak.R........    7 tests OK 
test_ncdf4_plot_peak.R........    7 tests OK 0.7s

test_quantMatrix.R............    0 tests    
test_quantMatrix.R............    0 tests    
test_quantMatrix.R............    0 tests    
test_quantMatrix.R............    0 tests    
test_quantMatrix.R............    0 tests    
test_quantMatrix.R............    0 tests    
test_quantMatrix.R............    1 tests OK 
test_quantMatrix.R............    2 tests OK 
test_quantMatrix.R............    2 tests OK 
test_quantMatrix.R............    2 tests OK 
test_quantMatrix.R............    3 tests OK 
test_quantMatrix.R............    4 tests OK 
test_quantMatrix.R............    4 tests OK 
test_quantMatrix.R............    4 tests OK 
test_quantMatrix.R............    5 tests OK 
test_quantMatrix.R............    5 tests OK 
test_quantMatrix.R............    5 tests OK 
test_quantMatrix.R............    6 tests OK 92ms

test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    0 tests    
test_ri_data_extract.R........    1 tests OK 
test_ri_data_extract.R........    1 tests OK 
test_ri_data_extract.R........    1 tests OK 
test_ri_data_extract.R........    2 tests OK 
test_ri_data_extract.R........    2 tests OK 
test_ri_data_extract.R........    2 tests OK 
test_ri_data_extract.R........    3 tests OK 
test_ri_data_extract.R........    3 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    4 tests OK 
test_ri_data_extract.R........    5 tests OK 
test_ri_data_extract.R........    5 tests OK 
test_ri_data_extract.R........    6 tests OK 1.2s

test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........    0 tests    
test_ri_plot_peak.R...........   10 tests OK 
test_ri_plot_peak.R...........   11 tests OK 
test_ri_plot_peak.R...........   12 tests OK 
test_ri_plot_peak.R...........   12 tests OK 0.2s

test_tsLib.R..................    0 tests    
test_tsLib.R..................    0 tests    
test_tsLib.R..................    0 tests    
test_tsLib.R..................    0 tests    
test_tsLib.R..................    0 tests    
test_tsLib.R..................    0 tests    
test_tsLib.R..................    0 tests    
test_tsLib.R..................    1 tests OK 
test_tsLib.R..................    2 tests OK 
test_tsLib.R..................    2 tests OK 
test_tsLib.R..................    2 tests OK 
test_tsLib.R..................    3 tests OK 
test_tsLib.R..................    4 tests OK 
test_tsLib.R..................    4 tests OK 
test_tsLib.R..................    5 tests OK 
test_tsLib.R..................    6 tests OK 
test_tsLib.R..................    7 tests OK 
test_tsLib.R..................    8 tests OK 
test_tsLib.R..................    9 tests OK 
test_tsLib.R..................   10 tests OK 
test_tsLib.R..................   11 tests OK 
test_tsLib.R..................   12 tests OK 0.1s

test_tsRim.R..................    0 tests    
test_tsRim.R..................    1 tests OK 
test_tsRim.R..................    2 tests OK 
test_tsRim.R..................    2 tests OK 
test_tsRim.R..................    3 tests OK 
test_tsRim.R..................    4 tests OK 
test_tsRim.R..................    4 tests OK 
test_tsRim.R..................    5 tests OK 
test_tsRim.R..................    6 tests OK 6ms

test_tsSample.R...............    0 tests    
test_tsSample.R...............    0 tests    
test_tsSample.R...............    0 tests    
test_tsSample.R...............    1 tests OK 
test_tsSample.R...............    2 tests OK 
test_tsSample.R...............    3 tests OK 
test_tsSample.R...............    3 tests OK 
test_tsSample.R...............    3 tests OK 
test_tsSample.R...............    3 tests OK 
test_tsSample.R...............    4 tests OK 
test_tsSample.R...............    5 tests OK 
test_tsSample.R...............    6 tests OK 
test_tsSample.R...............    6 tests OK 
test_tsSample.R...............    7 tests OK 
test_tsSample.R...............    8 tests OK 
test_tsSample.R...............    9 tests OK 73ms
All ok, 62 results (2.7s)
> 
> proc.time()
   user  system elapsed 
  1.789   0.186   3.559 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.0390.0090.087
FindAllPeaks1.5040.0752.737
FindPeaks0.3880.0150.711
ImportFameSettings0.0130.0020.023
ImportLibrary0.0290.0020.049
ImportSamples0.0130.0020.019
NetCDFPeakFinding0.3710.0410.890
Profile1.4180.0472.569
ProfileCleanUp1.2690.0452.338
RIcorrect16.154 1.18530.591
TSExample1.7510.1793.399
Write.Results0.0630.0090.135
baseline0.4630.0250.838
baselineCorrection0.4830.0220.909
baselineCorrectionQuant0.5280.0210.986
checkRimLim1.8490.0873.436
file0.1220.0130.240
fixRI1.7440.0853.206
medianRILib0.7750.0291.424
ncdf4Convert-method0.0860.0100.171
ncdf4_convert0.0260.0020.056
ncdf4_convert_from_path3.6530.3847.239
ncdf4_data_extract0.5710.0421.090
ncdf4_plot_peak1.6520.1403.173
ncdf4_update_ri0.4790.0320.884
peakCDFextraction0.8890.0571.660
peakFind0.4020.0250.775
plotFAME0.0090.0050.022
plotPeak0.3750.0180.687
plotPeakRI1.1510.0482.146
plotPeakSimple0.7090.0311.322
plotRIdev0.5530.0311.057
plotSpectra0.4040.0180.752
quantMatrix1.2460.0412.309
ri2rt0.0040.0000.007
riMatrix1.5590.0692.905
ri_data_extract0.0830.0050.160
ri_plot_peak2.2760.0944.197
rt2ri0.0030.0000.004
sampleRI0.7930.0301.464
tsLib-class0.0220.0030.045
tsMSdata-class0.0090.0210.053
tsProfile-class0.0090.0030.021
tsRim-class0.0030.0000.004
tsSample-class0.0340.0040.069
tsUpdate-method0.0000.0010.000
updateRI1.0190.1112.012
writeLibText0.0270.0020.049
writeMSP0.0200.0050.048