BioC 3.3: CHECK report for TargetSearch on linux2.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TargetSearch_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TargetSearch.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.27.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/16s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
RIcorrect 8.024  0.312    8.43
* 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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c file.c -o file.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c find_peaks.c -o find_peaks.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c getLine.c -o getLine.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hpf.c -o hpf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ncdf.c -o ncdf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c netcdf_peak_finding.c -o netcdf_peak_finding.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c peakExtraction.c -o peakExtraction.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ppc.c -o ppc.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.049	0.001	0.051
FindPeaks	0.240	0.000	0.251
ImportFameSettings	0.007	0.000	0.007
ImportLibrary	0.014	0.000	0.014
ImportSamples	0.003	0.000	0.003
NetCDFPeakFinding	0.226	0.034	0.269
Profile	0.750	0.021	0.764
ProfileCleanUp	0.711	0.005	0.710
RIcorrect	8.024	0.312	8.430
fixRI	1.109	0.029	1.135
medianRILib	0.420	0.013	0.430
peakFind	0.225	0.008	0.233
plotFAME	0.011	0.000	0.011
plotPeak	0.167	0.013	0.179
plotPeakSimple	0.280	0.012	0.291
plotRIdev	0.380	0.001	0.377
plotSpectra	0.221	0.004	0.224
quantMatrix	0.684	0.022	0.699
ri2rt	0.005	0.000	0.005
riMatrix	0.565	0.028	0.593
rt2ri	0.000	0.004	0.005
sampleRI	0.447	0.000	0.444
tsLib-class	0.005	0.000	0.005
tsMSdata-class	0.002	0.000	0.001
tsProfile-class	0.001	0.000	0.001
tsRim-class	0.002	0.000	0.001
tsSample-class	0.011	0.000	0.011
writeLibText	0.025	0.004	0.029

BioC 3.3: CHECK report for TargetSearch on linux2.bioconductor.org

Summary

Command output