BioC 3.5: CHECK report for R453Plus1Toolbox on toluca2

Package: R453Plus1Toolbox

Version: 1.25.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.25.1.tar.gz

StartedAt: 2017-04-23 08:32:03 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:38:37 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 394.0 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_1.25.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.25.1’
* 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 ... 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: 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 7.205  0.166   7.444
htmlReport       5.389  0.226   5.829
* 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-3.5-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-3.5-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	0.499	0.035	0.544
AVASet	0.625	0.020	0.671
AnnotatedVariants-class	0.003	0.000	0.003
MapperSet-class	0.035	0.010	0.045
MapperSet	0.007	0.002	0.009
SFFContainer-class	0.002	0.000	0.002
SFFRead-class	0.002	0.000	0.002
alignShortReads	2.301	0.012	2.325
annotateVariants	0.003	0.000	0.003
assayDataAmp	0.007	0.001	0.007
ava2vcf	0.472	0.035	0.508
avaSetExample	0.016	0.003	0.020
avaSetFiltered	0.022	0.003	0.026
avaSetFiltered_annot	0.002	0.001	0.003
breakpoints	0.006	0.001	0.008
calculateTiTv	0.013	0.002	0.016
captureArray	0.002	0.001	0.003
coverageOnTarget	0.384	0.035	0.422
demultiplexReads	0.317	0.003	0.322
detectBreakpoints	1.860	0.021	1.893
fDataAmp	0.019	0.002	0.022
featureDataAmp	0.018	0.002	0.019
filterChimericReads	2.475	0.038	2.546
genomeSequencerMIDs	0.024	0.001	0.024
getAlignedReads	0.108	0.003	0.111
getVariantPercentages	0.062	0.002	0.065
htmlReport	5.389	0.226	5.829
mapperSetExample	0.007	0.001	0.009
mergeBreakpoints	7.205	0.166	7.444
mutationInfo	0.004	0.001	0.004
plotAmpliconCoverage	0	0	0
plotChimericReads	3.331	0.011	3.364
plotVariants	0.007	0.001	0.008
plotVariationFrequency	0.000	0.000	0.001
qualityReportSFF	0.001	0.000	0.001
readSFF	0.075	0.001	0.078
readsOnTarget	0.346	0.012	0.369
referenceSequences	0.010	0.002	0.012
regions	0.004	0.001	0.005
removeLinker	0.027	0.001	0.029
sequenceCaptureLinkers	0.005	0.001	0.005
setVariantFilter	0.141	0.003	0.152
variants	0.003	0.001	0.005
writeSFF	0.110	0.001	0.112