Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:21 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


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 2023/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 2.0.0  (landing page)
Alvaro Cuadros-Inostroza
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/TargetSearch
git_branch: RELEASE_3_16
git_last_commit: 2fbc9bc
git_last_commit_date: 2022-11-01 11:04:26 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TargetSearch
Version: 2.0.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TargetSearch_2.0.0.tar.gz
StartedAt: 2023-04-11 00:29:27 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:30:34 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 66.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TargetSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings TargetSearch_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/TargetSearch.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘2.0.0’
* 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
* 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 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 7.624  0.228   7.951
* 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 ...
  ‘RICorrection.Rnw’... OK
  ‘TargetSearch.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.



Installation output

TargetSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL TargetSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘TargetSearch’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c baseline.c -o baseline.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c detection.c -o detection.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c file.c -o file.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c find_peaks.c -o find_peaks.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c getLine.c -o getLine.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hpf.c -o hpf.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matrix.c -o matrix.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ncdf.c -o ncdf.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c peak.c -o peak.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/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 -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 0.1s

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 0.3s

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 85ms

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 0.2s

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 63ms

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 50ms

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 4ms

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 30ms
All ok, 62 results (0.8s)
> 
> proc.time()
   user  system elapsed 
  1.048   0.063   1.097 

Example timings

TargetSearch.Rcheck/TargetSearch-Ex.timings

nameusersystemelapsed
FAMEoutliers0.0270.0080.036
FindAllPeaks0.3460.0200.371
FindPeaks0.0960.0000.096
ImportFameSettings0.0110.0000.012
ImportLibrary0.0230.0000.022
ImportSamples0.0090.0000.010
NetCDFPeakFinding0.1090.0190.128
Profile0.5130.0010.513
ProfileCleanUp0.3670.0080.375
RIcorrect7.6240.2287.951
TSExample1.4760.0281.505
Write.Results0.0550.0000.055
baseline0.2250.0000.224
baselineCorrection0.2050.0040.210
baselineCorrectionQuant0.3680.0000.368
checkRimLim0.5620.0160.578
file0.0580.0000.059
fixRI0.5540.0280.582
medianRILib0.1880.0040.192
ncdf4Convert-method0.0590.0000.058
ncdf4_convert0.0190.0000.019
ncdf4_convert_from_path1.4110.0841.495
ncdf4_data_extract0.2650.0000.265
ncdf4_plot_peak0.6960.0320.728
ncdf4_update_ri0.1890.0040.193
peakCDFextraction0.2900.0120.301
peakFind0.0980.0000.099
plotFAME0.0080.0000.007
plotPeak0.1580.0120.170
plotPeakRI0.2520.0080.260
plotPeakSimple0.1930.0040.197
plotRIdev0.2160.0120.228
plotSpectra0.1050.0040.109
quantMatrix0.3480.0040.353
ri2rt0.0030.0000.003
riMatrix0.4640.0440.508
ri_data_extract0.0230.0000.023
ri_plot_peak0.5360.0000.537
rt2ri0.0030.0000.002
sampleRI0.2020.0000.202
tsLib-class0.0170.0000.016
tsMSdata-class0.0080.0040.011
tsProfile-class0.0070.0000.007
tsRim-class0.0020.0000.002
tsSample-class0.0180.0000.017
tsUpdate-method000
updateRI0.8690.0240.894
writeLibText0.0190.0000.019
writeMSP0.0130.0000.014