BioC 3.2: CHECK report for R453Plus1Toolbox on oaxaca

Package: R453Plus1Toolbox

Version: 1.19.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.19.1.tar.gz

StartedAt: 2015-08-24 03:01:13 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:07:37 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 384.6 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 R453Plus1Toolbox_1.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.19.1’
* 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 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 ... [31s/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 ... NOTE
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
.annotateVariants_MapperSet: no visible binding for global variable
  ‘Hsapiens’
.ava2vcf: no visible binding for global variable ‘Hsapiens’
.detectBreakpoints: no visible binding for global variable ‘Hsapiens’
.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’
annotateVariants,MapperSet-BSgenome: no visible binding for global
  variable ‘Hsapiens’
annotateVariants,MapperSet-missing: no visible binding for global
  variable ‘Hsapiens’
ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’
detectBreakpoints,list: no visible binding for global variable
  ‘Hsapiens’
subset,AVASet : .local: no visible binding for global variable
  ‘referenceSeqID’
* 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 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 ... [40s/45s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mergeBreakpoints  7.982  0.201   9.817
htmlReport        5.285  0.239   6.078
plotChimericReads 4.713  0.009   5.234
* 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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/Library/Frameworks/R.framework/Resources/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-3.2-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	0.399	0.008	0.456
AVASet	0.195	0.004	0.224
AnnotatedVariants-class	0.003	0.001	0.004
MapperSet-class	0.040	0.009	0.052
MapperSet	0.009	0.000	0.011
SFFContainer-class	0.003	0.000	0.002
SFFRead-class	0.002	0.001	0.004
alignShortReads	2.080	0.008	2.387
annotateVariants	0.003	0.000	0.002
assayDataAmp	0.006	0.001	0.007
ava2vcf	0.340	0.015	0.409
avaSetExample	0.019	0.003	0.023
avaSetFiltered	0.031	0.004	0.041
avaSetFiltered_annot	0.002	0.000	0.003
breakpoints	0.004	0.000	0.005
calculateTiTv	0.015	0.002	0.020
captureArray	0.003	0.001	0.004
coverageOnTarget	0.194	0.017	0.235
demultiplexReads	0.136	0.002	0.154
detectBreakpoints	0.836	0.008	0.987
fDataAmp	0.022	0.001	0.023
featureDataAmp	0.025	0.002	0.027
filterChimericReads	2.600	0.021	2.905
genomeSequencerMIDs	0.047	0.001	0.052
getAlignedReads	0.132	0.002	0.150
getVariantPercentages	0.046	0.002	0.057
htmlReport	5.285	0.239	6.078
mapperSetExample	0.008	0.000	0.009
mergeBreakpoints	7.982	0.201	9.817
mutationInfo	0.004	0.001	0.004
plotAmpliconCoverage	0.001	0.000	0.000
plotChimericReads	4.713	0.009	5.234
plotVariants	0.007	0.000	0.008
plotVariationFrequency	0.001	0.000	0.000
qualityReportSFF	0.001	0.000	0.001
readSFF	0.097	0.001	0.099
readsOnTarget	0.405	0.012	0.450
referenceSequences	0.010	0.000	0.012
regions	0.004	0.000	0.005
removeLinker	0.030	0.001	0.032
sequenceCaptureLinkers	0.006	0.000	0.007
setVariantFilter	0.075	0.003	0.079
variants	0.004	0.000	0.005
writeSFF	0.046	0.000	0.049