BioC 2.12: CHECK report for R453Plus1Toolbox on petty

Package: R453Plus1Toolbox

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.10.0.tar.gz

StartedAt: 2013-10-08 23:34:53 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:44:41 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 588.1 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.10.0'
* 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 ... [49s/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [70s/80s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mergeBreakpoints  14.760  1.136  21.484
htmlReport         9.427  0.461  13.147
plotChimericReads  9.211  0.028   9.340
* 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-2.12-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  -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  -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-2.12-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	1.088	0.035	1.138
AVASet	0.356	0.011	0.375
AnnotatedVariants-class	0.019	0.003	0.023
MapperSet-class	0.070	0.014	0.089
MapperSet	0.022	0.004	0.026
SFFContainer-class	0.022	0.008	0.031
SFFRead-class	0.016	0.006	0.022
alignShortReads	2.235	0.013	2.375
annotateVariants	0.508	0.015	0.534
assayDataAmp	0.012	0.007	0.020
ava2vcf	0.498	0.038	0.550
avaSetExample	0.037	0.010	0.049
avaSetFiltered	0.068	0.017	0.086
avaSetFiltered_annot	0.006	0.004	0.011
breakpoints	0.008	0.004	0.012
calculateTiTv	0.026	0.007	0.035
captureArray	0.005	0.005	0.011
coverageOnTarget	0.720	0.044	0.827
demultiplexReads	0.165	0.011	0.208
detectBreakpoints	0.980	0.031	1.039
fDataAmp	0.045	0.008	0.052
featureDataAmp	0.042	0.008	0.051
filterChimericReads	3.558	0.051	3.703
genomeSequencerMIDs	0.071	0.006	0.086
getAlignedReads	0.231	0.016	0.258
getVariantPercentages	0.103	0.014	0.128
htmlReport	9.427	0.461	13.147
mapperSetExample	0.016	0.004	0.043
mergeBreakpoints	14.760	1.136	21.484
mutationInfo	0.007	0.004	0.012
plotAmpliconCoverage	0.003	0.006	0.010
plotChimericReads	9.211	0.028	9.340
plotVariants	0.019	0.024	0.043
plotVariationFrequency	0.002	0.003	0.005
qualityReportSFF	0.003	0.005	0.008
readSFF	0.237	0.010	0.247
readsOnTarget	1.329	0.049	1.385
referenceSequences	0.020	0.006	0.026
regions	0.008	0.006	0.014
removeLinker	0.075	0.016	0.091
sequenceCaptureLinkers	0.022	0.004	0.027
setVariantFilter	0.169	0.016	0.186
variants	0.018	0.013	0.030
writeSFF	0.051	0.006	0.057