BioC 2.12: CHECK report for R453Plus1Toolbox on george2

Package: R453Plus1Toolbox

Version: 1.10.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.10.0.tar.gz

StartedAt: 2013-10-09 04:18:06 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:27:46 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 579.7 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 3.0.1 (2013-05-16)
* 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 ‘1.10.0’
* 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 ... [50s/52s] 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 ... [67s/67s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  15.697  0.196  16.053
plotChimericReads  7.240  0.000   7.244
htmlReport         6.336  0.156   6.547
* 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
** testing if installed package can be loaded
Warning: replacing previous import ‘boxplot’ when loading ‘graphics’
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	1.460	0.016	1.493
AVASet	0.284	0.020	0.304
AnnotatedVariants-class	0.036	0.004	0.042
MapperSet-class	0.084	0.008	0.090
MapperSet	0.020	0.000	0.022
SFFContainer-class	0.044	0.000	0.043
SFFRead-class	0.028	0.004	0.029
alignShortReads	3.820	0.000	3.852
annotateVariants	0.028	0.016	0.041
assayDataAmp	0.952	0.008	0.960
ava2vcf	0.408	0.048	0.456
avaSetExample	0.016	0.024	0.041
avaSetFiltered	0.064	0.016	0.081
avaSetFiltered_annot	0.008	0.004	0.010
breakpoints	0.016	0.000	0.013
calculateTiTv	0.032	0.000	0.030
captureArray	0.004	0.008	0.010
coverageOnTarget	0.580	0.032	0.621
demultiplexReads	0.172	0.004	0.178
detectBreakpoints	0.912	0.004	0.927
fDataAmp	0.048	0.000	0.049
featureDataAmp	0.052	0.004	0.057
filterChimericReads	2.969	0.016	3.007
genomeSequencerMIDs	0.068	0.000	0.066
getAlignedReads	0.212	0.004	0.217
getVariantPercentages	0.092	0.012	0.107
htmlReport	6.336	0.156	6.547
mapperSetExample	0.024	0.000	0.023
mergeBreakpoints	15.697	0.196	16.053
mutationInfo	0.008	0.004	0.012
plotAmpliconCoverage	0.012	0.000	0.012
plotChimericReads	7.240	0.000	7.244
plotVariants	0.040	0.000	0.043
plotVariationFrequency	0.008	0.000	0.006
qualityReportSFF	0.008	0.000	0.007
readSFF	0.193	0.004	0.197
readsOnTarget	1.016	0.008	1.027
referenceSequences	0.024	0.000	0.024
regions	0.016	0.000	0.015
removeLinker	0.064	0.000	0.063
sequenceCaptureLinkers	0.020	0.000	0.021
setVariantFilter	0.164	0.016	0.207
variants	0.012	0.000	0.010
writeSFF	0.056	0.004	0.059