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: 2013-03-24 09:12:40 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:21:11 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 510.9 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.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 '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 ... [42s/45s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [60s/63s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  14.010  1.383  15.722
htmlReport         7.579  0.463   9.495
plotChimericReads  6.588  0.034   6.676
* 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
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 readSFF.c -o readSFF.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 writeSFF.c -o writeSFF.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 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
** 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	0.983	0.037	1.026
AVASet	0.296	0.015	0.380
AnnotatedVariants-class	0.022	0.008	0.034
MapperSet-class	0.060	0.019	0.108
MapperSet	0.019	0.004	0.024
SFFContainer-class	0.022	0.009	0.031
SFFRead-class	0.018	0.005	0.024
alignShortReads	2.214	0.021	2.436
annotateVariants	0.012	0.006	0.018
assayDataAmp	0.010	0.005	0.014
ava2vcf	0.383	0.057	0.443
avaSetExample	0.035	0.016	0.050
avaSetFiltered	0.058	0.020	0.078
avaSetFiltered_annot	0.005	0.005	0.010
breakpoints	0.007	0.005	0.013
calculateTiTv	0.022	0.008	0.031
captureArray	0.005	0.007	0.011
coverageOnTarget	0.547	0.054	0.612
demultiplexReads	0.142	0.015	0.176
detectBreakpoints	0.705	0.039	0.789
fDataAmp	0.032	0.009	0.040
featureDataAmp	0.032	0.010	0.042
filterChimericReads	2.728	0.060	2.839
genomeSequencerMIDs	0.071	0.007	0.083
getAlignedReads	0.243	0.015	0.291
getVariantPercentages	0.085	0.016	0.120
htmlReport	7.579	0.463	9.495
mapperSetExample	0.013	0.005	0.018
mergeBreakpoints	14.010	1.383	15.722
mutationInfo	0.007	0.007	0.013
plotAmpliconCoverage	0.014	0.023	0.037
plotChimericReads	6.588	0.034	6.676
plotVariants	0.018	0.025	0.042
plotVariationFrequency	0.003	0.003	0.007
qualityReportSFF	0.003	0.005	0.007
readSFF	0.157	0.009	0.168
readsOnTarget	0.954	0.040	1.003
referenceSequences	0.016	0.007	0.023
regions	0.007	0.006	0.013
removeLinker	0.053	0.017	0.070
sequenceCaptureLinkers	0.014	0.005	0.019
setVariantFilter	0.124	0.016	0.142
variants	0.015	0.012	0.027
writeSFF	0.040	0.007	0.053