Package: TargetSearch

Version: 1.6.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings TargetSearch_1.6.0.tar.gz

StartedAt: 2011-03-31 08:59:20 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 09:00:38 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 77.7 seconds

RetCode: 0

Status:  OK

CheckDir: TargetSearch.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/TargetSearch.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.6.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘TargetSearch’ can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘TargetSearch’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c getLine.c -o getLine.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c hpf.c -o hpf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c peakExtraction.c -o peakExtraction.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/TargetSearch.Rcheck/TargetSearch/libs
** R
** inst
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (TargetSearch)

name	user	system	elapsed
FAMEoutliers	0.144	0.000	0.153
FindPeaks	0.152	0.020	0.371
ImportFameSettings	0.008	0.000	0.008
ImportLibrary	0.012	0.000	0.026
ImportSamples	0.004	0.000	0.005
NetCDFPeakFinding	0.520	0.028	0.657
Profile	0.692	0.008	0.701
ProfileCleanUp	0.604	0.020	0.626
RIcorrect	25.517	0.612	27.060
medianRILib	0.320	0.012	0.333
peakFind	0.180	0.012	0.193
plotFAME	0.032	0.000	0.031
plotPeak	0.548	0.032	0.581
plotRIdev	0.460	0.008	0.469
plotSpectra	0.196	0.000	0.196
quantMatrix	0.600	0.008	0.610
ri2rt	0.008	0.000	0.008
rt2ri	0.008	0.000	0.008
sampleRI	0.364	0.008	0.370
tsLib-class	0.008	0.000	0.009
tsMSdata-class	0.000	0.000	0.001
tsProfile-class	0.000	0.000	0.001
tsRim-class	0.004	0.000	0.002
tsSample-class	0.028	0.004	0.030