Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:54 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for TargetSearch on machv2


To the developers/maintainers of the TargetSearch package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1933/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 1.50.1  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: RELEASE_3_14
git_last_commit: c3a63ea
git_last_commit_date: 2022-01-31 09:53:01 -0400 (Mon, 31 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TargetSearch
Version: 1.50.1
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_1.50.1.tar.gz
StartedAt: 2022-04-12 19:16:45 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:18:33 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 107.8 seconds
RetCode: 0
Status:   OK  
CheckDir: TargetSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.50.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TargetSearch.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘1.50.1’
* 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
* 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 18.186  1.458  19.825
* 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-3.14-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/4.1/Resources/library’
* installing *source* package ‘TargetSearch’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c baseline.c -o baseline.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c detection.c -o detection.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c file.c -o file.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c find_peaks.c -o find_peaks.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c getLine.c -o getLine.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hpf.c -o hpf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ncdf.c -o ncdf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c peak.c -o peak.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o TargetSearch.so Rinit.o baseline.o detection.o file.o find_peaks.o getLine.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/4.1/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
   ‘RICorrection.Rnw’ 
   ‘TargetSearch.Rnw’ 
** 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0.3s

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 0.6s

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 0.8s

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 0.1s
All ok, 29 results (1.9s)
> 
> proc.time()
   user  system elapsed 
  2.204   0.192   2.377 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.0690.0110.080
FindAllPeaks1.7680.0621.835
FindPeaks0.4900.0160.506
ImportFameSettings0.0100.0010.012
ImportLibrary0.0350.0010.037
ImportSamples0.0090.0010.011
NetCDFPeakFinding0.3970.0430.442
Profile1.8610.0421.905
ProfileCleanUp1.7200.0351.756
RIcorrect18.186 1.45819.825
TSExample2.3700.2452.659
checkRimLim1.7550.0961.857
file0.1660.0160.182
fixRI1.7790.0961.876
medianRILib1.0180.0331.053
ncdf4Convert-method0.1480.0090.158
ncdf4_convert0.0490.0080.057
ncdf4_convert_from_path0.0000.0000.001
ncdf4_data_extract0.0000.0000.001
ncdf4_plot_peak1.8450.1191.968
peakFind0.4450.0170.464
plotFAME0.0190.0050.023
plotPeak0.3650.0130.379
plotPeakRI1.5080.0471.559
plotPeakSimple0.8010.0400.843
plotRIdev0.7270.0240.752
plotSpectra0.4980.0140.513
quantMatrix1.6300.0431.674
ri2rt0.0050.0000.005
riMatrix1.6290.0781.709
ri_data_extract0.1040.0040.109
ri_plot_peak2.8360.0822.922
rt2ri0.0060.0000.006
sampleRI1.0300.0261.058
tsLib-class0.0260.0020.028
tsMSdata-class0.0010.0010.002
tsProfile-class0.0010.0000.002
tsRim-class0.0080.0010.010
tsSample-class0.0320.0050.036
tsUpdate-method0.0010.0000.001
updateRI1.5090.1081.620
writeLibText0.0280.0020.029