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CHECK report for R453Plus1Toolbox on tokay2

This page was generated on 2018-10-17 08:35:01 -0400 (Wed, 17 Oct 2018).

Package 1172/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.30.0
Hans-Ulrich Klein
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/R453Plus1Toolbox
Branch: RELEASE_3_7
Last Commit: 4c59153
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: R453Plus1Toolbox
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.30.0.tar.gz
StartedAt: 2018-10-17 04:13:09 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:20:41 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 451.9 seconds
RetCode: 0
Status:  OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:R453Plus1Toolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings R453Plus1Toolbox_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.30.0'
* 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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    extdata   2.5Mb
* 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
* 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 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mergeBreakpoints  6.5   0.11    6.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mergeBreakpoints 8.14   0.11    8.25
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.



Installation output

R453Plus1Toolbox.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/R453Plus1Toolbox_1.30.0.tar.gz && rm -rf R453Plus1Toolbox.buildbin-libdir && mkdir R453Plus1Toolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL R453Plus1Toolbox_1.30.0.zip && rm R453Plus1Toolbox_1.30.0.tar.gz R453Plus1Toolbox_1.30.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  686k  100  686k    0     0  8408k      0 --:--:-- --:--:-- --:--:-- 9155k

install for i386

* installing *source* package 'R453Plus1Toolbox' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c readSFF.c -o readSFF.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'R453Plus1Toolbox'
    finding HTML links ... done
    AVASet-class                            html  
    finding level-2 HTML links ... done

    AVASet                                  html  
    AnnotatedVariants-class                 html  
    Breakpoints-class                       html  
    MapperSet-class                         html  
    MapperSet                               html  
    SFFContainer-class                      html  
    SFFRead-class                           html  
    alignShortReads                         html  
    annotateVariants                        html  
    assayDataAmp                            html  
    ava2vcf                                 html  
    avaSetExample                           html  
    avaSetFiltered                          html  
    avaSetFiltered_annot                    html  
    baseFrequency                           html  
    baseQualityHist                         html  
    baseQualityStats                        html  
    breakpoints                             html  
    calculateTiTv                           html  
    captureArray                            html  
    complexity.dust                         html  
    complexity.entropy                      html  
    convertCigar                            html  
    coverageOnTarget                        html  
    demultiplexReads                        html  
    detectBreakpoints                       html  
    dinucleotideOddsRatio                   html  
    fDataAmp                                html  
    featureDataAmp                          html  
    filterChimericReads                     html  
    flowgramBarplot                         html  
    gcContent                               html  
    gcContentHist                           html  
    gcPerPosition                           html  
    genomeSequencerMIDs                     html  
    getAlignedReads                         html  
    getAminoAbbr                            html  
    getVariantPercentages                   html  
    homopolymerHist                         html  
    htmlReport                              html  
    mapperSetExample                        html  
    mergeBreakpoints                        html  
    mutationInfo                            html  
    nucleotideCharts                        html  
    plotAmpliconCoverage                    html  
    plotChimericReads                       html  
    plotVariants                            html  
    plotVariationFrequency                  html  
    positionQualityBoxplot                  html  
    qualityReportSFF                        html  
    readLengthHist                          html  
    readLengthStats                         html  
    readSFF                                 html  
    readsOnTarget                           html  
    referenceSequences                      html  
    regions                                 html  
    removeLinker                            html  
    sequenceCaptureLinkers                  html  
    sequenceQualityHist                     html  
    setVariantFilter                        html  
    sff2fastq                               html  
    variants                                html  
    writeSFF                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'R453Plus1Toolbox' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c readSFF.c -o readSFF.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'R453Plus1Toolbox' as R453Plus1Toolbox_1.30.0.zip
* DONE (R453Plus1Toolbox)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'R453Plus1Toolbox' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

R453Plus1Toolbox.Rcheck/examples_i386/R453Plus1Toolbox-Ex.timings

nameusersystemelapsed
AVASet-class0.310.000.45
AVASet0.220.060.28
AnnotatedVariants-class000
MapperSet-class0.050.000.05
MapperSet0.000.030.03
SFFContainer-class000
SFFRead-class000
alignShortReads2.280.052.33
annotateVariants000
assayDataAmp0.020.000.01
ava2vcf0.170.000.18
avaSetExample0.010.000.01
avaSetFiltered0.020.000.02
avaSetFiltered_annot000
breakpoints0.010.000.02
calculateTiTv0.020.000.01
captureArray000
coverageOnTarget0.250.001.64
demultiplexReads0.120.030.18
detectBreakpoints0.630.471.09
fDataAmp0.020.000.01
featureDataAmp0.030.010.05
filterChimericReads3.020.033.05
genomeSequencerMIDs0.010.000.01
getAlignedReads0.090.000.17
getVariantPercentages0.040.040.07
htmlReport2.590.513.32
mapperSetExample0.020.000.02
mergeBreakpoints6.500.116.61
mutationInfo0.000.020.01
plotAmpliconCoverage000
plotChimericReads2.010.002.02
plotVariants0.020.000.02
plotVariationFrequency000
qualityReportSFF000
readSFF0.120.000.20
readsOnTarget0.060.000.06
referenceSequences0.020.000.01
regions0.010.000.02
removeLinker0.020.000.01
sequenceCaptureLinkers000
setVariantFilter0.040.020.06
variants0.000.010.02
writeSFF0.050.000.04

R453Plus1Toolbox.Rcheck/examples_x64/R453Plus1Toolbox-Ex.timings

nameusersystemelapsed
AVASet-class0.320.020.33
AVASet0.220.010.23
AnnotatedVariants-class0.010.000.01
MapperSet-class0.050.000.05
MapperSet0.010.000.01
SFFContainer-class000
SFFRead-class000
alignShortReads2.040.022.05
annotateVariants000
assayDataAmp0.010.000.02
ava2vcf0.20.00.2
avaSetExample0.020.000.02
avaSetFiltered0.020.020.03
avaSetFiltered_annot000
breakpoints0.010.000.01
calculateTiTv0.010.000.01
captureArray0.000.010.02
coverageOnTarget0.240.000.23
demultiplexReads0.060.000.08
detectBreakpoints0.730.040.78
fDataAmp0.020.000.01
featureDataAmp0.020.000.02
filterChimericReads4.290.004.31
genomeSequencerMIDs0.020.000.01
getAlignedReads0.110.000.11
getVariantPercentages0.030.000.03
htmlReport3.090.473.63
mapperSetExample0.020.010.03
mergeBreakpoints8.140.118.25
mutationInfo000
plotAmpliconCoverage000
plotChimericReads2.280.022.30
plotVariants0.020.000.01
plotVariationFrequency000
qualityReportSFF000
readSFF0.090.000.10
readsOnTarget0.050.010.06
referenceSequences0.010.000.02
regions000
removeLinker0.020.000.02
sequenceCaptureLinkers000
setVariantFilter0.060.000.06
variants0.000.020.01
writeSFF0.030.000.04