Package: R453Plus1Toolbox

Version: 1.6.1

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.6.1.tar.gz

StartedAt: 2012-09-24 03:08:53 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 03:13:38 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 285.6 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.6.1’
* 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 whether package ‘R453Plus1Toolbox’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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’
* 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 ... OK
* 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
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c readSFF.c -o readSFF.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o R453Plus1Toolbox.so readSFF.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-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	0.096	0.008	0.108
AVASet	0.02	0.00	0.02
AnnotatedVariants-class	0.004	0.000	0.003
MapperSet-class	0.036	0.004	0.039
MapperSet	0.008	0.000	0.009
SFFContainer-class	0.000	0.000	0.001
SFFRead-class	0.004	0.000	0.001
alignShortReads	1.844	0.000	1.882
annotateVariants	0.000	0.000	0.001
assayDataAmp	0.004	0.004	0.006
avaSetExample	0.020	0.000	0.021
avaSetFiltered	0.044	0.004	0.048
avaSetFiltered_annot	0.000	0.000	0.003
breakpoints	0.004	0.000	0.004
calculateTiTv	0.016	0.004	0.019
captureArray	0.004	0.000	0.002
coverageOnTarget	0.400	0.008	0.413
demultiplexReads	0.552	0.000	0.566
detectBreakpoints	0.584	0.004	0.620
fDataAmp	0.028	0.000	0.027
featureDataAmp	0.020	0.000	0.021
filterChimericReads	2.061	0.004	2.129
genomeSequencerMIDs	0.056	0.000	0.056
getAlignedReads	0.188	0.000	0.197
getVariantPercentages	0.052	0.000	0.053
htmlReport	4.720	0.100	5.043
mapperSetExample	0.008	0.000	0.010
mergeBreakpoints	8.092	0.172	8.482
mutationInfo	0.004	0.000	0.003
plotAmpliconCoverage	0	0	0
plotChimericReads	4.777	0.016	4.869
plotVariants	0.004	0.000	0.004
plotVariationFrequency	0	0	0
readSFF	0	0	0
readsOnTarget	0.624	0.004	0.633
referenceSequences	0.008	0.000	0.009
regions	0.004	0.000	0.003
removeLinker	0.032	0.000	0.032
sequenceCaptureLinkers	0.004	0.000	0.007
setVariantFilter	0.084	0.004	0.089
variants	0.004	0.000	0.003