Package: R453Plus1Toolbox

Version: 1.9.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.9.5.tar.gz

StartedAt: 2013-03-25 04:13:25 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:20:06 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 400.7 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.9.5'
* 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 'R453Plus1Toolbox' can be installed ... [30s/31s] 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 ... NOTE
.getEnsemblInfo: no visible binding for global variable 'cds_length'
.getEnsemblInfo: no visible binding for global variable
  'ensembl_transcript_id'
.getMutations: no visible binding for global variable 'PatternStart'
.getMutations: no visible binding for global variable 'PatternEnd'
.htmlReport: no visible binding for global variable 'VarFreqForward'
.htmlReport: no visible binding for global variable 'VarFreqReverse'
.plotVariants: no visible binding for global variable 'mutation'
qualityReportSFF: no visible binding for '<<-' assignment to 'tmp'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  10.916  1.125  12.105
htmlReport         6.944  0.442   7.686
plotChimericReads  6.401  0.027   6.430
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.

* installing *source* package 'R453Plus1Toolbox' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c readSFF.c -o readSFF.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c writeSFF.c -o writeSFF.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 R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'boxplot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
   'vignette.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'boxplot' when loading 'graphics'
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.608	0.041	0.649
AVASet	0.207	0.022	0.234
AnnotatedVariants-class	0.013	0.010	0.024
MapperSet-class	0.049	0.021	0.070
MapperSet	0.019	0.006	0.025
SFFContainer-class	0.015	0.012	0.028
SFFRead-class	0.259	0.010	0.269
alignShortReads	1.145	0.013	1.174
annotateVariants	0.014	0.011	0.025
assayDataAmp	0.269	0.007	0.277
ava2vcf	0.312	0.025	0.338
avaSetExample	0.037	0.010	0.047
avaSetFiltered	0.063	0.018	0.082
avaSetFiltered_annot	0.004	0.004	0.009
breakpoints	0.006	0.004	0.010
calculateTiTv	0.024	0.007	0.032
captureArray	0.004	0.005	0.009
coverageOnTarget	0.419	0.031	0.449
demultiplexReads	0.099	0.009	0.108
detectBreakpoints	0.559	0.029	0.599
fDataAmp	0.027	0.007	0.036
featureDataAmp	0.025	0.007	0.032
filterChimericReads	2.276	0.035	2.314
genomeSequencerMIDs	0.050	0.006	0.056
getAlignedReads	0.154	0.011	0.166
getVariantPercentages	0.065	0.018	0.083
htmlReport	6.944	0.442	7.686
mapperSetExample	0.017	0.007	0.023
mergeBreakpoints	10.916	1.125	12.105
mutationInfo	0.005	0.005	0.010
plotAmpliconCoverage	0.003	0.006	0.009
plotChimericReads	6.401	0.027	6.430
plotVariants	0.015	0.020	0.035
plotVariationFrequency	0.002	0.005	0.007
qualityReportSFF	0.005	0.013	0.018
readSFF	0.126	0.008	0.134
readsOnTarget	1.179	0.032	1.212
referenceSequences	0.016	0.007	0.023
regions	0.007	0.005	0.012
removeLinker	0.045	0.009	0.054
sequenceCaptureLinkers	0.010	0.004	0.014
setVariantFilter	0.101	0.013	0.114
variants	0.006	0.005	0.011
writeSFF	0.033	0.008	0.042