Package: TargetSearch

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TargetSearch_1.7.1.tar.gz

StartedAt: 2011-02-24 21:39:43 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:41:38 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 115.0 seconds

RetCode: 0

Status:  OK

CheckDir: TargetSearch.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/TargetSearch.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.7.1’
* 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 ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘TargetSearch’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Rinit.c -o Rinit.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c find_peaks.c -o find_peaks.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c getLine.c -o getLine.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c hpf.c -o hpf.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c netcdf_peak_finding.c -o netcdf_peak_finding.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c peakExtraction.c -o peakExtraction.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c ppc.c -o ppc.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o TargetSearch.so Rinit.o find_peaks.o getLine.o hpf.o netcdf_peak_finding.o peakExtraction.o ppc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/TargetSearch.Rcheck/TargetSearch/libs/i386
** 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	0.203	0.009	0.235
FindPeaks	0.221	0.033	0.436
ImportFameSettings	0.012	0.002	0.015
ImportLibrary	0.028	0.002	0.046
ImportSamples	0.007	0.001	0.009
NetCDFPeakFinding	0.823	0.093	1.045
Profile	0.943	0.063	1.011
ProfileCleanUp	0.823	0.051	0.880
RIcorrect	43.923	4.144	49.263
medianRILib	0.414	0.028	0.444
peakFind	0.251	0.019	0.272
plotFAME	0.050	0.004	0.058
plotPeak	1.289	0.163	1.467
plotRIdev	0.722	0.036	0.770
plotSpectra	0.259	0.019	0.280
quantMatrix	0.798	0.049	0.856
ri2rt	0.012	0.000	0.013
rt2ri	0.012	0.000	0.012
sampleRI	0.482	0.032	0.516
tsLib-class	0.012	0.001	0.012
tsMSdata-class	0.002	0.001	0.002
tsProfile-class	0.002	0.000	0.002
tsRim-class	0.003	0.001	0.004
tsSample-class	0.045	0.004	0.050