Package: pdInfoBuilder

Version: 1.18.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch pdInfoBuilder_1.18.0.tar.gz

StartedAt: 2012-01-09 04:50:05 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:52:02 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 117.0 seconds

RetCode: 0

Status:  OK

CheckDir: pdInfoBuilder.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pdInfoBuilder/DESCRIPTION' ... OK
* this is package 'pdInfoBuilder' version '1.18.0'
* 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 'pdInfoBuilder' 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
* 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
combinePgfClfProbesetsMps: no visible binding for global variable
  'ptype'
parseNgsTrio: no visible binding for global variable 'mismatch'
parseProbeSequenceFile: no visible binding for global variable 'count'
* 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 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 ... 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

* installing *source* package 'pdInfoBuilder' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c pdInfoBuilder.c -o pdInfoBuilder.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o pdInfoBuilder.dll tmp.def pdInfoBuilder.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/pdInfoBuilder.Rcheck/pdInfoBuilder/libs/x64
** R
** inst
** preparing package for lazy loading
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'BuildingPDInfoPkgs.Rnw' 
   'howto-AffymetrixMapping.Rnw' 
** testing if installed package can be loaded
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================

* DONE (pdInfoBuilder)

name	user	system	elapsed
AffyExpressionPDInfoPkgSeed-class	0	0	0
AffySNPCNVPDInfoPkgSeed-class	0	0	0
AffySNPCNVPDInfoPkgSeed2-class	0	0	0
AffySNPPDInfoPkgSeed-class	0.65	0.00	0.66
AffySNPPDInfoPkgSeed2-class	0	0	0
AffySTPDInfoPkgSeed-class	0.02	0.00	0.02
AffyTilingPDInfoPkgSeed-class	0	0	0
NgsExpressionPDInfoPkgSeed-class	0	0	0
NgsTilingPDInfoPkgSeed-class	0	0	0
NimbleGenPDInfoPkgSeed-class	0	0	0
makePdInfoPackage	0	0	0