BioC 2.14: CHECK report for R453Plus1Toolbox on morelia

Package: R453Plus1Toolbox

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.14.0.tar.gz

StartedAt: 2014-10-08 00:58:02 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:04:25 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 383.6 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.14.0’
* 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 ... [32s/32s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/46s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mergeBreakpoints  8.739  0.104   8.995
htmlReport        5.599  0.274   6.147
plotChimericReads 5.640  0.013   5.692
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c readSFF.c -o readSFF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c writeSFF.c -o writeSFF.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.14-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.774	0.008	0.784
AVASet	0.244	0.008	0.252
AnnotatedVariants-class	0.003	0.001	0.004
MapperSet-class	0.047	0.010	0.058
MapperSet	0.010	0.001	0.011
SFFContainer-class	0.002	0.000	0.003
SFFRead-class	0.002	0.001	0.002
alignShortReads	1.943	0.010	2.178
annotateVariants	0.003	0.000	0.003
assayDataAmp	0.006	0.001	0.007
ava2vcf	0.403	0.035	0.439
avaSetExample	0.022	0.001	0.023
avaSetFiltered	0.036	0.001	0.036
avaSetFiltered_annot	0.003	0.001	0.003
breakpoints	0.004	0.000	0.004
calculateTiTv	0.016	0.000	0.017
captureArray	0.003	0.001	0.003
coverageOnTarget	0.281	0.019	0.300
demultiplexReads	0.182	0.003	0.186
detectBreakpoints	1.210	0.017	1.264
fDataAmp	0.023	0.001	0.026
featureDataAmp	0.023	0.001	0.024
filterChimericReads	3.011	0.019	3.080
genomeSequencerMIDs	0.044	0.000	0.044
getAlignedReads	0.162	0.002	0.163
getVariantPercentages	0.055	0.001	0.057
htmlReport	5.599	0.274	6.147
mapperSetExample	0.009	0.000	0.009
mergeBreakpoints	8.739	0.104	8.995
mutationInfo	0.004	0.001	0.004
plotAmpliconCoverage	0.001	0.000	0.001
plotChimericReads	5.640	0.013	5.692
plotVariants	0.007	0.000	0.008
plotVariationFrequency	0.000	0.000	0.001
qualityReportSFF	0.001	0.000	0.000
readSFF	0.133	0.003	0.136
readsOnTarget	0.907	0.009	0.918
referenceSequences	0.011	0.001	0.011
regions	0.004	0.001	0.004
removeLinker	0.041	0.000	0.042
sequenceCaptureLinkers	0.009	0.000	0.010
setVariantFilter	0.091	0.002	0.094
variants	0.002	0.000	0.003
writeSFF	0.049	0.000	0.051