BioC 2.11: CHECK report for R453Plus1Toolbox on perceval

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.8.1'
* 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 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'
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mergeBreakpoints  9.081  1.547  11.263
htmlReport        5.652  0.512   6.574
plotChimericReads 6.034  0.027   6.181
* 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
  '/Users/biocbuild/bbs-2.11-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.

* installing *source* package 'R453Plus1Toolbox' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c readSFF.c -o readSFF.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386
** 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	0.662	0.020	0.685
AVASet	0.495	0.007	0.504
AnnotatedVariants-class	0.002	0.001	0.001
MapperSet-class	0.035	0.010	0.046
MapperSet	0.008	0.001	0.010
SFFContainer-class	0.001	0.001	0.001
SFFRead-class	0.000	0.000	0.001
alignShortReads	1.546	0.008	1.581
annotateVariants	0.001	0.000	0.002
assayDataAmp	0.006	0.001	0.007
ava2vcf	0.301	0.028	0.334
avaSetExample	0.022	0.002	0.023
avaSetFiltered	0.035	0.001	0.037
avaSetFiltered_annot	0.002	0.001	0.003
breakpoints	0.005	0.001	0.005
calculateTiTv	0.015	0.001	0.017
captureArray	0.001	0.001	0.003
coverageOnTarget	0.818	0.024	0.860
demultiplexReads	0.096	0.003	0.099
detectBreakpoints	0.603	0.024	0.633
fDataAmp	0.024	0.001	0.030
featureDataAmp	0.023	0.001	0.025
filterChimericReads	2.141	0.031	2.257
genomeSequencerMIDs	0.045	0.001	0.046
getAlignedReads	0.166	0.006	0.176
getVariantPercentages	0.059	0.002	0.061
htmlReport	5.652	0.512	6.574
mapperSetExample	0.009	0.002	0.011
mergeBreakpoints	9.081	1.547	11.263
mutationInfo	0.004	0.001	0.004
plotAmpliconCoverage	0.000	0.001	0.001
plotChimericReads	6.034	0.027	6.181
plotVariants	0.004	0.001	0.004
plotVariationFrequency	0	0	0
readSFF	0	0	0
readsOnTarget	0.718	0.018	0.747
referenceSequences	0.010	0.002	0.012
regions	0.004	0.001	0.004
removeLinker	0.035	0.001	0.041
sequenceCaptureLinkers	0.008	0.001	0.009
setVariantFilter	0.094	0.003	0.097
variants	0.004	0.001	0.005

Summary

Command output