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: 2011-03-17 17:41:26 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:43:06 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 99.2 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) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 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 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
*** 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	0.109	0.006	0.128
FindPeaks	0.452	0.016	0.512
ImportFameSettings	0.008	0.001	0.009
ImportLibrary	0.018	0.002	0.020
ImportSamples	0.005	0.001	0.006
NetCDFPeakFinding	0.620	0.052	0.764
Profile	1.580	0.043	1.623
ProfileCleanUp	1.477	0.027	1.504
RIcorrect	33.468	1.761	35.593
medianRILib	0.888	0.018	0.905
peakFind	0.472	0.010	0.482
plotFAME	0.036	0.001	0.037
plotPeak	0.778	0.071	0.850
plotRIdev	0.810	0.016	0.826
plotSpectra	0.477	0.008	0.486
quantMatrix	1.461	0.024	1.486
ri2rt	0.01	0.00	0.01
rt2ri	0.010	0.000	0.009
sampleRI	0.937	0.016	0.953
tsLib-class	0.008	0.001	0.009
tsMSdata-class	0.001	0.000	0.001
tsProfile-class	0.001	0.000	0.001
tsRim-class	0.002	0.001	0.003
tsSample-class	0.033	0.002	0.035