BioC 2.13: CHECK report for R453Plus1Toolbox on perceval

Package: R453Plus1Toolbox

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.12.0.tar.gz

StartedAt: 2014-04-05 03:40:52 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:49:26 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 514.0 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [41s/44s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [62s/70s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  12.906  1.334  15.115
htmlReport         7.058  0.536  10.568
plotChimericReads  7.351  0.058   8.234
* 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c readSFF.c -o readSFF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c writeSFF.c -o writeSFF.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	1.672	0.065	1.977
AVASet	0.232	0.011	0.265
AnnotatedVariants-class	0.024	0.005	0.035
MapperSet-class	0.072	0.020	0.106
MapperSet	0.016	0.003	0.019
SFFContainer-class	0.021	0.005	0.026
SFFRead-class	0.016	0.005	0.021
alignShortReads	2.753	0.017	2.854
annotateVariants	0.019	0.007	0.025
assayDataAmp	0.665	0.013	0.681
ava2vcf	0.386	0.039	0.426
avaSetExample	0.023	0.005	0.028
avaSetFiltered	0.034	0.006	0.041
avaSetFiltered_annot	0.004	0.005	0.009
breakpoints	0.006	0.004	0.011
calculateTiTv	0.018	0.008	0.026
captureArray	0.004	0.005	0.008
coverageOnTarget	0.315	0.039	0.356
demultiplexReads	0.176	0.031	0.231
detectBreakpoints	0.899	0.033	1.005
fDataAmp	0.031	0.007	0.039
featureDataAmp	0.028	0.007	0.036
filterChimericReads	3.375	0.049	3.555
genomeSequencerMIDs	0.053	0.006	0.064
getAlignedReads	0.155	0.011	0.173
getVariantPercentages	0.089	0.017	0.111
htmlReport	7.058	0.536	10.568
mapperSetExample	0.011	0.005	0.015
mergeBreakpoints	12.906	1.334	15.115
mutationInfo	0.006	0.007	0.013
plotAmpliconCoverage	0.013	0.018	0.032
plotChimericReads	7.351	0.058	8.234
plotVariants	0.017	0.022	0.048
plotVariationFrequency	0.003	0.007	0.010
qualityReportSFF	0.003	0.005	0.009
readSFF	0.144	0.010	0.169
readsOnTarget	1.032	0.039	1.192
referenceSequences	0.015	0.007	0.024
regions	0.007	0.006	0.026
removeLinker	0.038	0.007	0.086
sequenceCaptureLinkers	0.024	0.014	0.038
setVariantFilter	0.115	0.017	0.133
variants	0.007	0.006	0.021
writeSFF	0.057	0.010	0.068