Package: flagme

Version: 1.15.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flagme_1.15.1.tar.gz

StartedAt: 2013-03-24 04:57:41 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:00:22 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 160.3 seconds

RetCode: 0

Status:  OK

CheckDir: flagme.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flagme.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flagme/DESCRIPTION' ... OK
* this is package 'flagme' version '1.15.1'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flagme' can be installed ... [11s/12s] 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 ... [49s/52s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
parseChromaTOF 7.880  0.057   8.442
parseELU       5.978  0.113   6.971
* 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 'flagme' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c dp.c -o dp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flagme.so dp.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'flagme'
** help
*** installing help indices
** building package indices
** installing vignettes
   'flagme.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (flagme)

name	user	system	elapsed
addAMDISPeaks	1.554	0.111	1.773
addChromaTOFPeaks	0.661	0.064	0.736
betweenAlignment	0.006	0.013	0.020
calcTimeDiffs	2.001	0.201	2.290
clusterAlignment	2.159	0.166	2.367
compress	2.235	0.165	2.443
dp	2.317	0.167	2.531
gatherInfo	2.366	0.170	2.593
imputePeaks	3.276	0.237	3.723
multipleAlignment	2.230	0.165	2.434
normDotProduct	2.098	0.158	2.272
parseChromaTOF	7.880	0.057	8.442
parseELU	5.978	0.113	6.971
peaksAlignment	0.007	0.007	0.015
peaksDataset	0.752	0.132	1.085
plot	1.493	0.198	1.837
plotImage	0.473	0.095	0.602
progressiveAlignment	2.389	0.174	2.626
rmaFitUnit	2.297	0.181	2.503