BioC 3.2: CHECK report for TargetSearch on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TargetSearch_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/TargetSearch.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.26.0’
* 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 ... [3s/3s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/18s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
RIcorrect 8.902  0.397   9.366
* 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: OK

* installing *source* package ‘TargetSearch’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c file.c -o file.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c find_peaks.c -o find_peaks.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c getLine.c -o getLine.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hpf.c -o hpf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ncdf.c -o ncdf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c netcdf_peak_finding.c -o netcdf_peak_finding.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c peakExtraction.c -o peakExtraction.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ppc.c -o ppc.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o TargetSearch.so Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/TargetSearch.Rcheck/TargetSearch/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TargetSearch)

name	user	system	elapsed
FAMEoutliers	0.045	0.001	0.069
FindPeaks	0.302	0.003	0.353
ImportFameSettings	0.01	0.00	0.01
ImportLibrary	0.012	0.004	0.016
ImportSamples	0.005	0.000	0.005
NetCDFPeakFinding	0.326	0.020	0.360
Profile	0.904	0.020	0.922
ProfileCleanUp	0.803	0.036	0.836
RIcorrect	8.902	0.397	9.366
fixRI	0.918	0.032	0.949
medianRILib	0.468	0.000	0.467
peakFind	0.239	0.012	0.250
plotFAME	0.015	0.000	0.015
plotPeak	0.183	0.004	0.186
plotPeakSimple	0.309	0.084	0.392
plotRIdev	0.413	0.012	0.423
plotSpectra	0.253	0.000	0.252
quantMatrix	0.832	0.004	0.831
ri2rt	0.004	0.000	0.005
riMatrix	0.704	0.032	0.741
rt2ri	0.005	0.000	0.005
sampleRI	0.577	0.019	0.646
tsLib-class	0.006	0.000	0.006
tsMSdata-class	0.001	0.000	0.001
tsProfile-class	0.001	0.000	0.001
tsRim-class	0.003	0.000	0.002
tsSample-class	0.011	0.004	0.016
writeLibText	0.031	0.004	0.034

BioC 3.2: CHECK report for TargetSearch on zin1

Summary

Command output