Package: R453Plus1Toolbox

Version: 1.4.0

Command: rm -rf R453Plus1Toolbox.buildbin-libdir && mkdir R453Plus1Toolbox.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R453Plus1Toolbox.buildbin-libdir R453Plus1Toolbox_1.4.0.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_1.4.0.tar.gz && mv R453Plus1Toolbox.buildbin-libdir/* R453Plus1Toolbox.Rcheck/ && rmdir R453Plus1Toolbox.buildbin-libdir

StartedAt: 2012-03-24 02:34:38 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:40:21 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 343.2 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 2.14.2 (2012-02-29)
* 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 '1.4.0'
* 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 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 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 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 compiled code ... 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'R453Plus1Toolbox' ...
Warning in file.copy(instdir, lockdir, recursive = TRUE) :
  problem copying na 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 ual 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 na 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 ual 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 na 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 ual 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 na 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 ual 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 rics.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 rics.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 gDir.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 Metrics.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 Metrics.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 sAll.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 sAll.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 l 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 og 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
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c readSFF.c -o readSFF.o
gcc -m64 -shared -s -static-libgcc -o R453Plus1Toolbox.dll tmp.def readSFF.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -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
* MD5 sums
packaged installation of 'R453Plus1Toolbox' as R453Plus1Toolbox_1.4.0.zip

* DONE (R453Plus1Toolbox)