Package: SIM

Version: 1.24.0

Command: rm -rf SIM.buildbin-libdir && mkdir SIM.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SIM.buildbin-libdir SIM_1.24.0.tar.gz >SIM-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=SIM.buildbin-libdir --install="check:SIM-install.out" --force-multiarch --no-vignettes --timings SIM_1.24.0.tar.gz && mv SIM.buildbin-libdir/* SIM.Rcheck/ && rmdir SIM.buildbin-libdir

StartedAt: 2012-03-24 02:55:52 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:58:51 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 179.0 seconds

RetCode: 0

Status:  OK

CheckDir: SIM.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/SIM.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 'SIM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIM' version '1.24.0'
* 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 'SIM' 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
assemble.data: no visible binding for global variable 'chrom.table'
convertGenomicRegion: no visible binding for global variable
  'chrom.table'
link.metadata: no visible binding for global variable 'expr.data'
link.metadata: no visible binding for global variable 'hgu133plus2CHR'
link.metadata: no visible binding for global variable
  'hgu133plus2CHRLOC'
link.metadata: no visible binding for global variable
  'hgu133plus2SYMBOL'
plotCytobands: no visible binding for global variable 'chrom.table'
sim.plot.pvals.on.genome: no visible binding for global variable
  'chrom.table'
sim.update.chrom.table: no visible global function definition for
  'dbConnect'
sim.update.chrom.table: no visible global function definition for
  'MySQL'
sim.update.chrom.table: no visible global function definition for
  'dbGetQuery'
* 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 ... NOTE
'library' or 'require' call not declared from: 'RColorBrewer'
* 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 'SIM' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c withinWindow.c -o withinWindow.o
gcc -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/SIM.buildbin-libdir/SIM/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for class "data.frameOrNULL" in package 'globaltest' seems equivalent to one from package 'Biobase' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'SIM.Rnw' using 'latin1' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'SIM' ...
** 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 withinWindow.c -o withinWindow.o
gcc -m64 -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.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/SIM.buildbin-libdir/SIM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIM' as SIM_1.24.0.zip

* DONE (SIM)