Package: R453Plus1Toolbox

Version: 1.9.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.9.2.tar.gz

StartedAt: 2013-01-16 05:36:42 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:43:21 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 399.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.9.2’
* 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 ... 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 ... WARNING
Found the following significant warnings:

  Warning: %in% between a RangedData and a RangedData object is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  10.305  0.072  10.503
plotChimericReads  5.576  0.000   5.578
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/loc/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  -c readSFF.c -o readSFF.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c writeSFF.c -o writeSFF.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/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	0.808	0.008	0.821
AVASet	0.216	0.000	0.215
AnnotatedVariants-class	0.016	0.000	0.016
MapperSet-class	0.040	0.012	0.053
MapperSet	0.020	0.000	0.021
SFFContainer-class	0.024	0.000	0.025
SFFRead-class	0.028	0.000	0.025
alignShortReads	2.153	0.004	2.178
annotateVariants	0.008	0.008	0.015
assayDataAmp	0.004	0.008	0.011
ava2vcf	0.288	0.048	0.333
avaSetExample	0.020	0.008	0.029
avaSetFiltered	0.048	0.004	0.053
avaSetFiltered_annot	0.004	0.004	0.006
breakpoints	0.004	0.004	0.008
calculateTiTv	0.016	0.004	0.019
captureArray	0.004	0.000	0.006
coverageOnTarget	0.416	0.008	0.429
demultiplexReads	0.116	0.000	0.116
detectBreakpoints	0.552	0.012	0.581
fDataAmp	0.028	0.000	0.028
featureDataAmp	0.024	0.004	0.028
filterChimericReads	2.184	0.008	2.197
genomeSequencerMIDs	0.056	0.000	0.053
getAlignedReads	0.216	0.004	0.221
getVariantPercentages	0.068	0.000	0.070
htmlReport	4.772	0.072	4.868
mapperSetExample	0.012	0.000	0.013
mergeBreakpoints	10.305	0.072	10.503
mutationInfo	0.008	0.000	0.007
plotAmpliconCoverage	0.004	0.000	0.004
plotChimericReads	5.576	0.000	5.578
plotVariants	0.016	0.000	0.019
plotVariationFrequency	0.004	0.000	0.003
qualityReportSFF	0.004	0.000	0.003
readSFF	0.140	0.000	0.143
readsOnTarget	0.792	0.004	0.795
referenceSequences	0.016	0.000	0.015
regions	0.004	0.000	0.008
removeLinker	0.048	0.000	0.049
sequenceCaptureLinkers	0.012	0.004	0.013
setVariantFilter	0.104	0.000	0.104
variants	0.012	0.000	0.015
writeSFF	0.036	0.000	0.037