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BioC 3.0: CHECK report for R453Plus1Toolbox on moscato1

This page was generated on 2015-04-10 09:46:41 -0700 (Fri, 10 Apr 2015).

Package 710/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.16.0
Hans-Ulrich Klein
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: R453Plus1Toolbox
Version: 1.16.0
Command: rm -rf R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && mkdir R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.16.0.tar.gz >R453Plus1Toolbox.Rcheck\00install.out 2>&1 && cp R453Plus1Toolbox.Rcheck\00install.out R453Plus1Toolbox-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=R453Plus1Toolbox.buildbin-libdir --install="check:R453Plus1Toolbox-install.out" --force-multiarch --no-vignettes --timings R453Plus1Toolbox_1.16.0.tar.gz
StartedAt: 2015-04-10 04:38:11 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:48:46 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 634.8 seconds
RetCode: 0
Status:  OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && mkdir R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.16.0.tar.gz >R453Plus1Toolbox.Rcheck\00install.out 2>&1 && cp R453Plus1Toolbox.Rcheck\00install.out R453Plus1Toolbox-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=R453Plus1Toolbox.buildbin-libdir --install="check:R453Plus1Toolbox-install.out" --force-multiarch --no-vignettes --timings R453Plus1Toolbox_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.16.0'
* 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 global function definition for 'getSeq'
.ava2vcf: no visible binding for global variable 'Hsapiens'
.ava2vcf: no visible global function definition for 'DataFrame'
.ava2vcf: no visible global function definition for 'DataFrameList'
.ava2vcf: no visible global function definition for 'SimpleList'
.ava2vcf: no visible global function definition for 'Rle'
.ava2vcf: no visible global function definition for 'CharacterList'
.baseFrequency: no visible global function definition for
  'alphabetFrequency'
.complexity.dust: no visible global function definition for
  'trinucleotideFrequency'
.complexity.entropy: no visible global function definition for
  'trinucleotideFrequency'
.detectBreakpoints: no visible binding for global variable 'Hsapiens'
.dinucleotideOddsRatio: no visible global function definition for
  'dinucleotideFrequency'
.dinucleotideOddsRatio: no visible global function definition for
  'oligonucleotideFrequency'
.filterChimericReads: no visible global function definition for
  'elementLengths'
.gcContent: no visible global function definition for
  'alphabetFrequency'
.gcContentHist: no visible global function definition for
  'alphabetFrequency'
.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'
readSFF: no visible global function definition for 'PhredQuality'
readSFF: no visible global function definition for
  'QualityScaledDNAStringSet'
addRead,SFFContainer-SFFRead: no visible global function definition for
  'PhredQuality'
addRead,SFFContainer-SFFRead: no visible global function definition for
  'QualityScaledDNAStringSet'
annotateVariants,MapperSet-BSgenome: no visible binding for global
  variable 'Hsapiens'
annotateVariants,MapperSet-missing: no visible binding for global
  variable 'Hsapiens'
ava2vcf,AVASet: no visible global function definition for 'getSeq'
ava2vcf,AVASet: no visible binding for global variable 'Hsapiens'
ava2vcf,AVASet: no visible global function definition for 'DataFrame'
ava2vcf,AVASet: no visible global function definition for
  'DataFrameList'
ava2vcf,AVASet: no visible global function definition for 'SimpleList'
ava2vcf,AVASet: no visible global function definition for 'Rle'
ava2vcf,AVASet: no visible global function definition for
  'CharacterList'
baseFrequency,DNAStringSet: no visible global function definition for
  'alphabetFrequency'
complexity.dust,DNAStringSet: no visible global function definition for
  'trinucleotideFrequency'
complexity.entropy,DNAStringSet: no visible global function definition
  for 'trinucleotideFrequency'
detectBreakpoints,list: no visible binding for global variable
  'Hsapiens'
dinucleotideOddsRatio,DNAStringSet: no visible global function
  definition for 'dinucleotideFrequency'
dinucleotideOddsRatio,DNAStringSet: no visible global function
  definition for 'oligonucleotideFrequency'
filterChimericReads,list-RangesList-DNAString-missing-missing: no
  visible global function definition for 'elementLengths'
filterChimericReads,list-RangesList-DNAString-numeric-numeric: no
  visible global function definition for 'elementLengths'
filterChimericReads,list-RangesList-missing-missing-missing: no visible
  global function definition for 'elementLengths'
filterChimericReads,list-RangesList-missing-numeric-numeric: no visible
  global function definition for 'elementLengths'
filterChimericReads,list-missing-DNAString-missing-missing: no visible
  global function definition for 'elementLengths'
filterChimericReads,list-missing-DNAString-numeric-numeric: no visible
  global function definition for 'elementLengths'
filterChimericReads,list-missing-missing-missing-missing: no visible
  global function definition for 'elementLengths'
filterChimericReads,list-missing-missing-numeric-numeric: no visible
  global function definition for 'elementLengths'
gcContent,DNAStringSet: no visible global function definition for
  'alphabetFrequency'
gcContentHist,DNAStringSet: no visible global function definition for
  'alphabetFrequency'
sff2fastq,SFFContainer: no visible global function definition for
  'writeXStringSet'
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.0-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/i386/R453Plus1Toolbox.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/x64/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' ... [64s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mergeBreakpoints 11.09   0.20   13.53
htmlReport        3.96   0.28    9.96
alignShortReads   1.40   0.03   13.80
** running examples for arch 'x64' ... [50s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mergeBreakpoints 9.98   0.05   10.03
htmlReport       5.04   0.41    8.71
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.

R453Plus1Toolbox.Rcheck/00install.out:


install for i386

* installing *source* package 'R453Plus1Toolbox' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c readSFF.c -o readSFF.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c writeSFF.c -o writeSFF.o
gcc -m32 -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o writeSFF.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: %in%, levels, paste, sapply, substr, substring
No methods found in "Biostrings" for requests: countIndex
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%, levels, paste, sapply, substr, substring
No methods found in "Biostrings" for requests: countIndex

install for x64

* installing *source* package 'R453Plus1Toolbox' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c readSFF.c -o readSFF.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c writeSFF.c -o writeSFF.o
gcc -m64 -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o writeSFF.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/x64
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%, levels, paste, sapply, substr, substring
No methods found in "Biostrings" for requests: countIndex
* MD5 sums
packaged installation of 'R453Plus1Toolbox' as R453Plus1Toolbox_1.16.0.zip
* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/examples_i386/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.500.011.88
AVASet0.160.000.16
AnnotatedVariants-class000
MapperSet-class0.030.000.03
MapperSet0.000.020.02
SFFContainer-class000
SFFRead-class000
alignShortReads 1.40 0.0313.80
annotateVariants000
assayDataAmp000
ava2vcf0.230.020.25
avaSetExample0.030.000.03
avaSetFiltered0.020.000.02
avaSetFiltered_annot0.020.000.01
breakpoints000
calculateTiTv0.010.000.02
captureArray000
coverageOnTarget0.170.010.18
demultiplexReads0.090.000.09
detectBreakpoints0.970.001.24
fDataAmp0.010.020.03
featureDataAmp0.030.000.03
filterChimericReads1.870.031.91
genomeSequencerMIDs0.040.000.03
getAlignedReads0.070.000.08
getVariantPercentages0.050.000.04
htmlReport3.960.289.96
mapperSetExample0.020.000.01
mergeBreakpoints11.09 0.2013.53
mutationInfo000
plotAmpliconCoverage0.020.000.01
plotChimericReads3.910.003.92
plotVariants000
plotVariationFrequency000
qualityReportSFF0.020.000.01
readSFF0.090.000.10
readsOnTarget0.720.020.73
referenceSequences000
regions000
removeLinker0.020.000.01
sequenceCaptureLinkers000
setVariantFilter0.070.000.06
variants0.000.010.01
writeSFF0.030.000.04

R453Plus1Toolbox.Rcheck/examples_x64/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.670.000.81
AVASet0.180.000.19
AnnotatedVariants-class000
MapperSet-class0.030.010.06
MapperSet0.020.000.02
SFFContainer-class000
SFFRead-class000
alignShortReads1.770.021.80
annotateVariants0.020.000.01
assayDataAmp000
ava2vcf0.30.00.3
avaSetExample0.030.000.03
avaSetFiltered0.030.000.03
avaSetFiltered_annot000
breakpoints0.010.000.02
calculateTiTv0.020.000.01
captureArray000
coverageOnTarget0.220.000.22
demultiplexReads0.120.000.13
detectBreakpoints1.190.011.20
fDataAmp0.020.000.02
featureDataAmp0.020.020.03
filterChimericReads2.380.012.40
genomeSequencerMIDs0.030.000.03
getAlignedReads0.10.00.1
getVariantPercentages0.040.000.04
htmlReport5.040.418.71
mapperSetExample0.020.000.01
mergeBreakpoints 9.98 0.0510.03
mutationInfo000
plotAmpliconCoverage000
plotChimericReads4.600.004.61
plotVariants0.020.000.01
plotVariationFrequency000
qualityReportSFF000
readSFF0.170.010.19
readsOnTarget1.020.021.03
referenceSequences000
regions000
removeLinker0.030.000.04
sequenceCaptureLinkers000
setVariantFilter0.080.010.09
variants000
writeSFF0.030.020.05