BioC 3.1: CHECK report for R453Plus1Toolbox on morelia

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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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.18.0’
* 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 ... [24s/24s] 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 ... [33s/34s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 6.446  0.321   7.114
htmlReport       4.444  0.471   5.339
* 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-3.1-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-3.1-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.276	0.010	0.286
AVASet	0.210	0.009	0.220
AnnotatedVariants-class	0.003	0.000	0.003
MapperSet-class	0.030	0.016	0.046
MapperSet	0.008	0.003	0.010
SFFContainer-class	0.003	0.000	0.003
SFFRead-class	0.003	0.001	0.003
alignShortReads	1.366	0.047	1.482
annotateVariants	0.002	0.000	0.002
assayDataAmp	0.003	0.000	0.004
ava2vcf	0.253	0.013	0.266
avaSetExample	0.019	0.002	0.021
avaSetFiltered	0.028	0.004	0.032
avaSetFiltered_annot	0.002	0.001	0.003
breakpoints	0.004	0.001	0.005
calculateTiTv	0.011	0.002	0.013
captureArray	0.002	0.001	0.003
coverageOnTarget	0.181	0.059	0.240
demultiplexReads	0.092	0.002	0.093
detectBreakpoints	0.640	0.069	0.710
fDataAmp	0.024	0.007	0.031
featureDataAmp	0.020	0.001	0.021
filterChimericReads	1.878	0.079	1.958
genomeSequencerMIDs	0.038	0.001	0.039
getAlignedReads	0.086	0.005	0.091
getVariantPercentages	0.046	0.002	0.048
htmlReport	4.444	0.471	5.339
mapperSetExample	0.005	0.002	0.007
mergeBreakpoints	6.446	0.321	7.114
mutationInfo	0.003	0.001	0.003
plotAmpliconCoverage	0.001	0.000	0.001
plotChimericReads	3.736	0.064	3.804
plotVariants	0.004	0.000	0.005
plotVariationFrequency	0.000	0.001	0.000
qualityReportSFF	0	0	0
readSFF	0.084	0.005	0.089
readsOnTarget	0.371	0.073	0.445
referenceSequences	0.006	0.000	0.006
regions	0.003	0.000	0.003
removeLinker	0.022	0.000	0.023
sequenceCaptureLinkers	0.004	0.000	0.004
setVariantFilter	0.056	0.002	0.058
variants	0.003	0.000	0.003
writeSFF	0.032	0.001	0.032

BioC 3.1: CHECK report for R453Plus1Toolbox on morelia

Summary

Command output