Package: TargetSearch

Version: 1.42.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TargetSearch_1.42.1.tar.gz

StartedAt: 2020-04-15 00:37:02 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:37:58 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 55.3 seconds

RetCode: 0

Status:  OK

CheckDir: TargetSearch.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TargetSearch.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TargetSearch_1.42.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/TargetSearch.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.42.1’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
RIcorrect 10.672  0.332  11.551
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TargetSearch
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘TargetSearch’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c baseline.c -o baseline.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c detection.c -o detection.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c file.c -o file.o
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c getLine.c -o getLine.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c hpf.c -o hpf.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c matrix.c -o matrix.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c ncdf.c -o ncdf.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c peak.c -o peak.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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)

name	user	system	elapsed
FAMEoutliers	0.044	0.004	0.048
FindAllPeaks	0.500	0.024	0.631
FindPeaks	0.104	0.000	0.103
ImportFameSettings	0.004	0.000	0.007
ImportLibrary	0.020	0.000	0.018
ImportSamples	0.012	0.000	0.016
NetCDFPeakFinding	0.180	0.028	0.466
Profile	0.572	0.000	0.572
ProfileCleanUp	0.468	0.004	0.472
RIcorrect	10.672	0.332	11.551
TSExample	2.240	0.048	2.296
checkRimLim	0.224	0.008	0.233
fixRI	0.900	0.028	0.948
medianRILib	0.336	0.000	0.338
ncdf4Convert-method	0.120	0.004	0.124
ncdf4_convert	0.040	0.004	0.043
ncdf4_convert_from_path	0	0	0
ncdf4_data_extract	0	0	0
peakFind	0.196	0.000	0.197
plotFAME	0.020	0.004	0.024
plotPeak	0.184	0.020	0.204
plotPeakRI	0.324	0.000	0.325
plotPeakSimple	0.396	0.008	0.415
plotRIdev	0.340	0.008	0.348
plotSpectra	0.208	0.000	0.206
quantMatrix	0.640	0.000	0.641
ri2rt	0.004	0.000	0.005
riMatrix	0.880	0.032	0.912
rt2ri	0.004	0.000	0.003
sampleRI	0.212	0.004	0.219
tsLib-class	0.016	0.000	0.016
tsMSdata-class	0.000	0.000	0.001
tsProfile-class	0.000	0.000	0.001
tsRim-class	0.000	0.000	0.001
tsSample-class	0.012	0.004	0.017
tsUpdate-method	0.004	0.000	0.000
writeLibText	0.016	0.000	0.016