Package: crlmm

Version: 1.11.2

Command: mkdir crlmm.buildbin-libdir && E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --no-multiarch --library=crlmm.buildbin-libdir crlmm_1.11.2.tar.gz

StartedAt: 2011-07-07 04:10:03 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:10:32 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 29.6 seconds

RetCode: 0

Status:  OK

PackageFile: crlmm_1.11.2.zip

PackageFileSize: 3.056 MiB

* installing *source* package 'crlmm' ...
** libs
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/include"          -O3 -Wall  -std=gnu99 -c gtypeCaller.c -o gtypeCaller.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/include"          -O3 -Wall  -std=gnu99 -c init.c -o init.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/include"          -O3 -Wall  -std=gnu99 -c trimmed.c -o trimmed.o
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/include"          -O3 -Wall  -std=gnu99 -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124:15: warning: unused variable 'n_ignore'
gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LE:/biocbld/bbs-2.9-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/crlmm.buildbin-libdir/crlmm/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")'.

================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Loading package bit1.1-7

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit

Loading package ff2.2-2
- getOption("fftempdir")=="E:/biocbld/bbs-2.9-bioc/tmpdir/RtmpaQqurr"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system

Creating a generic function for "lines" from package "graphics" in package "crlmm"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'AffymetrixPreprocessCN.Rnw' 
   'CopyNumberOverview.Rnw' 
   'IlluminaPreprocessCN.Rnw' 
   'Infrastructure.Rnw' 
   'copynumber.Rnw' 
   'crlmmDownstream.Rnw' 
   'genotyping.Rnw' 
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Welcome to crlmm version 1.11.2
* MD5 sums
packaged installation of 'crlmm' as crlmm_1.11.2.zip

* DONE (crlmm)