BioC 2.13: CHECK report for R453Plus1Toolbox on zin1

Package: R453Plus1Toolbox

Version: 1.12.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.12.0.tar.gz

StartedAt: 2014-04-05 03:19:42 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:24:36 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 294.1 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.12.0’
* 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 ... [24s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘Biobase’ ‘Biostrings’ ‘ShortRead’ ‘Rsamtools’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘BSgenome.Scerevisiae.UCSC.sacCer2’ ‘TeachingDemos’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 9.132  0.072   9.239
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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-2.13-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-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::boxplot’ when loading ‘R453Plus1Toolbox’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::boxplot’ when loading ‘R453Plus1Toolbox’
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.824	0.012	0.836
AVASet	0.168	0.004	0.171
AnnotatedVariants-class	0.008	0.000	0.008
MapperSet-class	0.044	0.000	0.044
MapperSet	0.008	0.000	0.010
SFFContainer-class	0.008	0.000	0.010
SFFRead-class	0.012	0.000	0.010
alignShortReads	1.232	0.000	1.249
annotateVariants	0.268	0.008	0.274
assayDataAmp	0.000	0.004	0.006
ava2vcf	0.276	0.012	0.288
avaSetExample	0.012	0.004	0.019
avaSetFiltered	0.024	0.008	0.031
avaSetFiltered_annot	0.004	0.000	0.004
breakpoints	0.000	0.004	0.006
calculateTiTv	0.008	0.008	0.016
captureArray	0.004	0.000	0.004
coverageOnTarget	0.172	0.012	0.184
demultiplexReads	0.128	0.000	0.186
detectBreakpoints	0.668	0.008	0.687
fDataAmp	0.020	0.000	0.021
featureDataAmp	0.024	0.000	0.022
filterChimericReads	2.493	0.008	2.506
genomeSequencerMIDs	0.036	0.000	0.038
getAlignedReads	0.116	0.000	0.202
getVariantPercentages	0.056	0.000	0.054
htmlReport	4.360	0.064	4.693
mapperSetExample	0.012	0.000	0.009
mergeBreakpoints	9.132	0.072	9.239
mutationInfo	0.004	0.000	0.003
plotAmpliconCoverage	0.004	0.000	0.001
plotChimericReads	4.817	0.000	4.824
plotVariants	0.008	0.000	0.007
plotVariationFrequency	0.000	0.000	0.001
qualityReportSFF	0.000	0.000	0.004
readSFF	0.112	0.000	0.111
readsOnTarget	0.664	0.012	0.679
referenceSequences	0.008	0.000	0.009
regions	0.004	0.000	0.003
removeLinker	0.028	0.000	0.027
sequenceCaptureLinkers	0.008	0.000	0.007
setVariantFilter	0.076	0.000	0.075
variants	0.004	0.000	0.004
writeSFF	0.040	0.000	0.042