Package: R453Plus1Toolbox

Version: 1.9.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.9.5.tar.gz

StartedAt: 2013-03-25 04:00:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:09:58 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 576.4 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [45s/46s] 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 ... [64s/69s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  15.181  0.212  17.719
plotChimericReads  7.076  0.004   7.205
htmlReport         6.816  0.156   7.772
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c readSFF.c -o readSFF.o
readSFF.c: In function ‘readSFF’:
readSFF.c:46:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c writeSFF.c -o writeSFF.o
gcc -std=gnu99 -shared -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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	1.316	0.028	1.354
AVASet	0.304	0.008	0.326
AnnotatedVariants-class	0.024	0.000	0.024
MapperSet-class	0.068	0.004	0.074
MapperSet	0.032	0.000	0.030
SFFContainer-class	0.024	0.000	0.024
SFFRead-class	0.036	0.000	0.043
alignShortReads	3.480	0.004	3.577
annotateVariants	0.020	0.008	0.029
assayDataAmp	0.008	0.004	0.012
ava2vcf	0.336	0.096	0.430
avaSetExample	0.032	0.008	0.038
avaSetFiltered	0.056	0.008	0.063
avaSetFiltered_annot	0.012	0.000	0.008
breakpoints	0.000	0.012	0.010
calculateTiTv	0.020	0.004	0.027
captureArray	0.000	0.012	0.011
coverageOnTarget	0.632	0.008	0.647
demultiplexReads	0.152	0.000	0.154
detectBreakpoints	0.824	0.016	0.842
fDataAmp	0.032	0.004	0.037
featureDataAmp	0.048	0.000	0.048
filterChimericReads	3.088	0.016	3.104
genomeSequencerMIDs	0.088	0.000	0.087
getAlignedReads	0.252	0.012	0.262
getVariantPercentages	0.133	0.000	0.132
htmlReport	6.816	0.156	7.772
mapperSetExample	0.020	0.000	0.025
mergeBreakpoints	15.181	0.212	17.719
mutationInfo	0.012	0.004	0.013
plotAmpliconCoverage	0.012	0.000	0.011
plotChimericReads	7.076	0.004	7.205
plotVariants	0.040	0.000	0.041
plotVariationFrequency	0.004	0.000	0.004
qualityReportSFF	0.004	0.000	0.005
readSFF	0.196	0.000	0.196
readsOnTarget	1.040	0.004	1.047
referenceSequences	0.020	0.004	0.024
regions	0.008	0.000	0.010
removeLinker	0.060	0.000	0.061
sequenceCaptureLinkers	0.024	0.000	0.022
setVariantFilter	0.132	0.008	0.139
variants	0.024	0.000	0.025
writeSFF	0.048	0.004	0.053