Package: R453Plus1Toolbox

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.30.0.tar.gz

StartedAt: 2018-10-16 23:29:55 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:35:53 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 358.1 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 --install=check:R453Plus1Toolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R453Plus1Toolbox_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.30.0’
* 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 ... 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 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: no visible binding for global variable ‘referenceSeqID’
Undefined global functions or variables:
  Hsapiens PatternEnd PatternStart VarFreqForward VarFreqReverse
  cds_length ensembl_transcript_id mutation 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 8.534  0.193   8.816
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL R453Plus1Toolbox
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c readSFF.c -o readSFF.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/R453Plus1Toolbox/libs
** R
** data
** inst
** byte-compile and prepare 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	0.290	0.009	0.312
AVASet	0.202	0.008	0.210
AnnotatedVariants-class	0.003	0.000	0.004
MapperSet-class	0.044	0.015	0.062
MapperSet	0.010	0.003	0.012
SFFContainer-class	0.005	0.000	0.005
SFFRead-class	0.004	0.000	0.004
alignShortReads	1.805	0.015	1.836
annotateVariants	0.003	0.001	0.003
assayDataAmp	0.008	0.002	0.009
ava2vcf	0.283	0.009	0.292
avaSetExample	0.014	0.001	0.015
avaSetFiltered	0.019	0.001	0.021
avaSetFiltered_annot	0.004	0.002	0.006
breakpoints	0.008	0.003	0.011
calculateTiTv	0.012	0.002	0.015
captureArray	0.003	0.002	0.006
coverageOnTarget	0.233	0.026	0.259
demultiplexReads	0.117	0.014	0.134
detectBreakpoints	0.993	0.095	1.098
fDataAmp	0.018	0.003	0.023
featureDataAmp	0.014	0.002	0.016
filterChimericReads	3.774	0.041	3.840
genomeSequencerMIDs	0.028	0.000	0.029
getAlignedReads	0.086	0.003	0.089
getVariantPercentages	0.038	0.003	0.040
htmlReport	4.191	0.445	4.666
mapperSetExample	0.008	0.002	0.011
mergeBreakpoints	8.534	0.193	8.816
mutationInfo	0.004	0.002	0.007
plotAmpliconCoverage	0.001	0.000	0.001
plotChimericReads	2.814	0.031	2.872
plotVariants	0.012	0.001	0.012
plotVariationFrequency	0.001	0.000	0.001
qualityReportSFF	0.001	0.001	0.001
readSFF	0.116	0.001	0.118
readsOnTarget	0.081	0.003	0.085
referenceSequences	0.013	0.003	0.016
regions	0.005	0.003	0.007
removeLinker	0.028	0.001	0.029
sequenceCaptureLinkers	0.008	0.000	0.008
setVariantFilter	0.068	0.005	0.072
variants	0.006	0.002	0.007
writeSFF	0.047	0.001	0.048