BioC 2.12: CHECK report for TargetSearch on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/TargetSearch.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.15.2’
* 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 ... OK
* checking installed package size ... OK
* checking package 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
RIcorrect 18.473   0.74  19.423
* 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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c file.c -o file.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c getLine.c -o getLine.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hpf.c -o hpf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ncdf.c -o ncdf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c peakExtraction.c -o peakExtraction.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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 file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/TargetSearch.Rcheck/TargetSearch/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RICorrection.Rnw’ 
   ‘TargetSearch.Rnw’ 
** testing if installed package can be loaded

* DONE (TargetSearch)

name	user	system	elapsed
FAMEoutliers	0.064	0.012	0.088
FindPeaks	0.192	0.012	0.288
ImportFameSettings	0.040	0.000	0.039
ImportLibrary	0.036	0.000	0.041
ImportSamples	0.036	0.000	0.035
NetCDFPeakFinding	1.008	0.048	1.074
Profile	0.692	0.028	0.719
ProfileCleanUp	0.596	0.048	0.644
RIcorrect	18.473	0.740	19.423
fixRI	1.780	0.076	1.859
medianRILib	0.320	0.020	0.339
peakFind	0.192	0.008	0.199
plotFAME	0.028	0.000	0.028
plotPeak	0.496	0.012	0.508
plotPeakSimple	0.900	0.056	0.956
plotRIdev	0.396	0.016	0.411
plotSpectra	0.192	0.004	0.203
quantMatrix	0.604	0.012	0.614
ri2rt	0.016	0.000	0.014
riMatrix	1.536	0.060	1.598
rt2ri	0.016	0.000	0.015
sampleRI	0.348	0.016	0.362
tsLib-class	0.024	0.000	0.026
tsMSdata-class	0.008	0.000	0.008
tsProfile-class	0.000	0.004	0.005
tsRim-class	0.008	0.000	0.010
tsSample-class	0.040	0.000	0.042
writeLibText	0.048	0.000	0.048

Summary

Command output