BioC 2.9: CHECK report for R453Plus1Toolbox on moscato1

Package: R453Plus1Toolbox

Version: 1.3.1

Command: mkdir R453Plus1Toolbox.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.3.1.tar.gz >R453Plus1Toolbox-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=R453Plus1Toolbox.buildbin-libdir --install="check:R453Plus1Toolbox-install.out" --force-multiarch --no-vignettes --timings R453Plus1Toolbox_1.3.1.tar.gz && mv R453Plus1Toolbox.buildbin-libdir/* R453Plus1Toolbox.Rcheck/ && rmdir R453Plus1Toolbox.buildbin-libdir

StartedAt: 2011-07-07 06:00:47 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:06:35 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 347.9 seconds

RetCode: 0

Status: OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-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 '1.3.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R453Plus1Toolbox' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.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'
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK


install for i386

* installing *source* package 'R453Plus1Toolbox' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c readSFF.c -o readSFF.o
gcc -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: BSgenome
Loading required package: GenomicRanges
Creating a new generic function for "name" in package "R453Plus1Toolbox"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded
Warning message:
multiple methods tables found for 'name' 

add DLL for x64

* installing *source* package 'R453Plus1Toolbox' ...
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.CAT.454Reads.fna to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.CAT.454Reads.fna: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.CAT.454Reads.qual to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.CAT.454Reads.qual: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.TCA.454Reads.fna to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.TCA.454Reads.fna: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.TCA.454Reads.qual to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\1.TCA.454Reads.qual: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.CAT.454Reads.fna to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.CAT.454Reads.fna: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.CAT.454Reads.qual to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.CAT.454Reads.qual: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.TCA.454Reads.fna to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.TCA.454Reads.fna: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.TCA.454Reads.qual to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\2.TCA.454Reads.qual: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454BaseCallerMetrics.csv to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454BaseCallerMetrics.csv: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454BaseCallerMetrics.txt to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454BaseCallerMetrics.txt: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454DataProcessingDir.xml to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454DataProcessingDir.xml: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454QualityFilterMetrics.csv to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454QualityFilterMetrics.csv: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454QualityFilterMetrics.txt to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454QualityFilterMetrics.txt: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454RuntimeMetricsAll.csv to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454RuntimeMetricsAll.csv: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454RuntimeMetricsAll.txt to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\454RuntimeMetricsAll.txt: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\dataRunParams.xml to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\dataRunParams.xml: No such file or directory
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\gsRunProcessor.log to D:\biocbld\bbs-2.9-bioc\meat\R453Plus1Toolbox.buildbin-libdir\00LOCK-R453Plus1Toolbox\R453Plus1Toolbox\extdata\StructuralVariantDetection\R_2009_07_30_14_26_52_FLX12080469_Administrator_714003\D_2009_07_31_08_45_30_flxcluster_fullProcessing_714003\gsRunProcessor.log: No such file or directory
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c readSFF.c -o readSFF.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/R453Plus1Toolbox.buildbin-libdir/R453Plus1Toolbox/libs/x64
** testing if installed package can be loaded
Warning message:
multiple methods tables found for 'name' 
* MD5 sums
packaged installation of 'R453Plus1Toolbox' as R453Plus1Toolbox_1.3.1.zip

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.08	0.00	0.08
AVASet	0.01	0.02	0.03
AnnotatedVariants-class	0	0	0
MapperSet-class	0.03	0.01	0.05
MapperSet	0	0	0
SFFContainer-class	0	0	0
SFFRead-class	0	0	0
alignShortReads	0.89	0.00	0.89
annotateVariants	0	0	0
assayDataAmp	0.01	0.00	0.02
avaSetExample	0.02	0.00	0.01
avaSetFiltered	0.05	0.00	0.05
avaSetFiltered_annot	0	0	0
breakpoints	0	0	0
calculateTiTv	0.02	0.00	0.01
captureArray	0	0	0
coverageOnTarget	0.53	0.03	0.56
demultiplexReads	0.09	0.00	0.09
detectBreakpoints	0.52	0.00	0.52
fDataAmp	0.03	0.00	0.03
featureDataAmp	0.01	0.00	0.02
filterChimericReads	1.83	0.03	1.85
genomeSequencerMIDs	0.04	0.00	0.05
getAlignedReads	0.18	0.00	0.17
getVariantPercentages	0.04	0.00	0.05
htmlReport	5.06	0.32	6.06
mapperSetExample	0.02	0.00	0.02
mergeBreakpoints	7.91	0.17	8.08
plotAmpliconCoverage	0	0	0
plotChimericReads	4.94	0.00	4.94
plotVariants	0	0	0
plotVariationFrequency	0	0	0
readSFF	0	0	0
readsOnTarget	0.58	0.01	0.60
referenceSequences	0.02	0.00	0.01
removeLinker	0.03	0.00	0.03
sequenceCaptureLinkers	0	0	0
setVariantFilter	0.11	0.00	0.11
transcriptdf	0	0	0

Summary

Command output