BioC 3.4: CHECK report for R453Plus1Toolbox on moscato1

Package: R453Plus1Toolbox

Version: 1.23.0

Command: rm -rf R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && mkdir R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.23.0.tar.gz >R453Plus1Toolbox.Rcheck\00install.out 2>&1 && cp R453Plus1Toolbox.Rcheck\00install.out R453Plus1Toolbox-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=R453Plus1Toolbox.buildbin-libdir --install="check:R453Plus1Toolbox-install.out" --force-multiarch --no-vignettes --timings R453Plus1Toolbox_1.23.0.tar.gz

StartedAt: 2016-09-20 14:45:13 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 14:53:34 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 500.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && mkdir R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.23.0.tar.gz >R453Plus1Toolbox.Rcheck\00install.out 2>&1 && cp R453Plus1Toolbox.Rcheck\00install.out R453Plus1Toolbox-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=R453Plus1Toolbox.buildbin-libdir --install="check:R453Plus1Toolbox-install.out" --force-multiarch --no-vignettes --timings R453Plus1Toolbox_1.23.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/i386/R453Plus1Toolbox.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mergeBreakpoints 7.14   0.08    9.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mergeBreakpoints 7.32   0.06    7.38
htmlReport       3.83   0.28    5.59
* 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, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'R453Plus1Toolbox' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c readSFF.c -o readSFF.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c writeSFF.c -o writeSFF.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o writeSFF.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'R453Plus1Toolbox' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c readSFF.c -o readSFF.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c writeSFF.c -o writeSFF.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o writeSFF.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R453Plus1Toolbox' as R453Plus1Toolbox_1.23.0.zip
* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.34	0.02	0.64
AVASet	0.24	0.00	0.24
AnnotatedVariants-class	0	0	0
MapperSet-class	0.05	0.00	0.05
MapperSet	0.01	0.00	0.01
SFFContainer-class	0	0	0
SFFRead-class	0.02	0.00	0.02
alignShortReads	1.89	0.00	2.34
annotateVariants	0	0	0
assayDataAmp	0.00	0.01	0.01
ava2vcf	0.18	0.00	0.19
avaSetExample	0.02	0.02	0.03
avaSetFiltered	0.03	0.00	0.03
avaSetFiltered_annot	0	0	0
breakpoints	0.00	0.01	0.02
calculateTiTv	0.01	0.00	0.01
captureArray	0.00	0.02	0.02
coverageOnTarget	0.13	0.00	0.12
demultiplexReads	0.11	0.00	0.14
detectBreakpoints	0.72	0.05	0.78
fDataAmp	0.01	0.01	0.04
featureDataAmp	0.03	0.00	0.03
filterChimericReads	2.39	0.00	2.39
genomeSequencerMIDs	0.01	0.00	0.01
getAlignedReads	0.08	0.00	0.08
getVariantPercentages	0.05	0.00	0.05
htmlReport	3.35	0.27	4.74
mapperSetExample	0.02	0.00	0.02
mergeBreakpoints	7.14	0.08	9.48
mutationInfo	0	0	0
plotAmpliconCoverage	0	0	0
plotChimericReads	2.59	0.01	2.60
plotVariants	0	0	0
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.07	0.00	0.08
readsOnTarget	0.36	0.00	0.36
referenceSequences	0.00	0.02	0.02
regions	0.02	0.00	0.01
removeLinker	0.01	0.00	0.02
sequenceCaptureLinkers	0.02	0.00	0.01
setVariantFilter	0.06	0.00	0.07
variants	0	0	0
writeSFF	0.03	0.00	0.03

name	user	system	elapsed
AVASet-class	0.28	0.02	0.29
AVASet	0.15	0.00	0.15
AnnotatedVariants-class	0.01	0.00	0.01
MapperSet-class	0.03	0.00	0.03
MapperSet	0.02	0.00	0.02
SFFContainer-class	0	0	0
SFFRead-class	0	0	0
alignShortReads	2.01	0.01	2.03
annotateVariants	0	0	0
assayDataAmp	0.02	0.00	0.01
ava2vcf	0.20	0.02	0.22
avaSetExample	0.01	0.00	0.02
avaSetFiltered	0.02	0.00	0.02
avaSetFiltered_annot	0	0	0
breakpoints	0.02	0.00	0.02
calculateTiTv	0.01	0.00	0.01
captureArray	0	0	0
coverageOnTarget	0.13	0.02	0.14
demultiplexReads	0.07	0.01	0.63
detectBreakpoints	0.64	0.03	0.67
fDataAmp	0.02	0.00	0.02
featureDataAmp	0.01	0.00	0.02
filterChimericReads	1.87	0.00	1.87
genomeSequencerMIDs	0.02	0.00	0.01
getAlignedReads	0.08	0.02	0.10
getVariantPercentages	0.03	0.00	0.03
htmlReport	3.83	0.28	5.59
mapperSetExample	0.01	0.00	0.01
mergeBreakpoints	7.32	0.06	7.38
mutationInfo	0	0	0
plotAmpliconCoverage	0	0	0
plotChimericReads	2.84	0.00	2.84
plotVariants	0	0	0
plotVariationFrequency	0	0	0
qualityReportSFF	0	0	0
readSFF	0.07	0.00	0.08
readsOnTarget	0.27	0.00	0.26
referenceSequences	0.02	0.00	0.02
regions	0	0	0
removeLinker	0.03	0.00	0.03
sequenceCaptureLinkers	0	0	0
setVariantFilter	0.07	0.00	0.08
variants	0	0	0
writeSFF	0.04	0.00	0.03