BioC 3.4: CHECK report for R453Plus1Toolbox on morelia

Package: R453Plus1Toolbox

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.23.0.tar.gz

StartedAt: 2016-09-20 11:47:47 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:52:15 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 268.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 1

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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_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.23.0’
* 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 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’
.baseQualityHist: no visible global function definition for ‘hist’
.complexity.dust: no visible global function definition for ‘hist’
.complexity.dust: no visible global function definition for ‘abline’
.complexity.entropy: no visible global function definition for ‘hist’
.complexity.entropy: no visible global function definition for ‘abline’
.detectBreakpoints: no visible binding for global variable ‘Hsapiens’
.dinucleotideOddsRatio: no visible global function definition for
  ‘abline’
.gcContentHist: no visible global function definition for ‘hist’
.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’
.readLengthHist: no visible global function definition for ‘hist’
.sequenceQualityHist: no visible global function definition for ‘hist’
.sequenceQualityHist_sr: no visible global function definition for
  ‘hist’
qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’
qualityReportSFF: no visible global function definition for ‘Sweave’
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’
baseQualityHist,QualityScaledDNAStringSet: no visible global function
  definition for ‘hist’
complexity.dust,DNAStringSet: no visible global function definition for
  ‘hist’
complexity.dust,DNAStringSet: no visible global function definition for
  ‘abline’
complexity.entropy,DNAStringSet: no visible global function definition
  for ‘hist’
complexity.entropy,DNAStringSet: no visible global function definition
  for ‘abline’
detectBreakpoints,list: no visible binding for global variable
  ‘Hsapiens’
dinucleotideOddsRatio,DNAStringSet: no visible global function
  definition for ‘abline’
gcContentHist,DNAStringSet: no visible global function definition for
  ‘hist’
plotVariants,AnnotatedVariants-character: no visible global function
  definition for ‘rainbow’
plotVariants,data.frame-character: no visible global function
  definition for ‘rainbow’
readLengthHist,DNAStringSet: no visible global function definition for
  ‘hist’
sequenceQualityHist,QualityScaledDNAStringSet: no visible global
  function definition for ‘hist’
sequenceQualityHist,ShortReadQ: no visible global function definition
  for ‘hist’
subset,AVASet: no visible binding for global variable ‘referenceSeqID’
Undefined global functions or variables:
  Hsapiens PatternEnd PatternStart Sweave VarFreqForward VarFreqReverse
  abline cds_length ensembl_transcript_id hist mutation rainbow
  referenceSeqID
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "hist")
  importFrom("utils", "Sweave")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'AVASet,ANY,ANY,ANY'
  generic '[' and siglist 'Breakpoints,ANY,ANY,ANY'
  generic '[' and siglist 'SFFContainer,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 4.446  0.146   5.073
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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-3.4-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	0.273	0.017	0.290
AVASet	0.126	0.004	0.128
AnnotatedVariants-class	0.002	0.000	0.001
MapperSet-class	0.024	0.006	0.029
MapperSet	0.006	0.001	0.006
SFFContainer-class	0.001	0.001	0.002
SFFRead-class	0.001	0.000	0.001
alignShortReads	1.729	0.008	1.814
annotateVariants	0.003	0.000	0.003
assayDataAmp	0.004	0.002	0.006
ava2vcf	0.183	0.004	0.187
avaSetExample	0.017	0.002	0.018
avaSetFiltered	0.026	0.004	0.029
avaSetFiltered_annot	0.003	0.001	0.004
breakpoints	0.004	0.001	0.006
calculateTiTv	0.011	0.001	0.012
captureArray	0.002	0.001	0.004
coverageOnTarget	0.177	0.033	0.210
demultiplexReads	0.111	0.014	0.126
detectBreakpoints	0.469	0.036	0.506
fDataAmp	0.015	0.001	0.016
featureDataAmp	0.020	0.001	0.021
filterChimericReads	1.622	0.027	1.649
genomeSequencerMIDs	0.032	0.001	0.032
getAlignedReads	0.117	0.003	0.119
getVariantPercentages	0.033	0.002	0.034
htmlReport	4.060	0.244	4.405
mapperSetExample	0.009	0.002	0.010
mergeBreakpoints	4.446	0.146	5.073
mutationInfo	0.004	0.001	0.005
plotAmpliconCoverage	0.001	0.000	0.001
plotChimericReads	2.259	0.018	2.277
plotVariants	0.005	0.000	0.005
plotVariationFrequency	0.001	0.000	0.000
qualityReportSFF	0.000	0.000	0.001
readSFF	0.080	0.002	0.082
readsOnTarget	0.286	0.017	0.304
referenceSequences	0.009	0.001	0.011
regions	0.002	0.001	0.003
removeLinker	0.019	0.001	0.020
sequenceCaptureLinkers	0.005	0.000	0.005
setVariantFilter	0.049	0.002	0.051
variants	0.004	0.001	0.006
writeSFF	0.027	0.000	0.027