Package: TargetSearch

Version: 1.10.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings TargetSearch_1.10.1.tar.gz

StartedAt: 2012-03-24 03:00:12 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:01:30 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 77.6 seconds

RetCode: 0

Status:  OK

CheckDir: TargetSearch.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/TargetSearch.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-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 ‘1.10.1’
* 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 whether package ‘TargetSearch’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘TargetSearch’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c find_peaks.c -o find_peaks.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c getLine.c -o getLine.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c hpf.c -o hpf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c netcdf_peak_finding.c -o netcdf_peak_finding.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c peakExtraction.c -o peakExtraction.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ppc.c -o ppc.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o TargetSearch.so Rinit.o find_peaks.o getLine.o hpf.o netcdf_peak_finding.o peakExtraction.o ppc.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/TargetSearch.Rcheck/TargetSearch/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘TargetSearch.Rnw’ 
** testing if installed package can be loaded

* DONE (TargetSearch)

name	user	system	elapsed
FAMEoutliers	0.060	0.004	0.074
FindPeaks	0.248	0.020	0.380
ImportFameSettings	0.008	0.000	0.009
ImportLibrary	0.008	0.000	0.015
ImportSamples	0.004	0.000	0.005
NetCDFPeakFinding	0.628	0.052	0.709
Profile	0.644	0.044	0.687
ProfileCleanUp	0.604	0.016	0.628
RIcorrect	24.409	0.944	25.569
medianRILib	0.332	0.004	0.337
peakFind	0.180	0.008	0.189
plotFAME	0.028	0.004	0.034
plotPeak	0.640	0.072	0.710
plotRIdev	0.392	0.016	0.406
plotSpectra	0.188	0.008	0.198
quantMatrix	0.584	0.028	0.610
ri2rt	0.008	0.000	0.006
rt2ri	0.008	0.000	0.007
sampleRI	0.344	0.012	0.358
tsLib-class	0.004	0.000	0.006
tsMSdata-class	0.000	0.000	0.001
tsProfile-class	0.000	0.000	0.001
tsRim-class	0.000	0.000	0.002
tsSample-class	0.028	0.000	0.026
writeLibText	0.056	0.000	0.055