Package: cn.farms

Version: 1.1.2

Command: mkdir cn.farms.buildbin-libdir && E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --no-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.1.2.tar.gz

StartedAt: 2011-07-07 04:09:20 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:09:40 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 20.9 seconds

RetCode: 0

Status:  OK

PackageFile: cn.farms_1.1.2.zip

PackageFileSize: 2.426 MiB

* installing *source* package 'cn.farms' ...
** libs
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/include"          -O3 -Wall  -std=gnu99 -c R_init_cnfarms.c -o R_init_cnfarms.o
g++  -I"E:/biocbld/bbs-2.9-bioc/R/include"          -O2 -Wall  -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:244:6: warning: unused variable 'method'
gcc  -I"E:/biocbld/bbs-2.9-bioc/R/include"          -O3 -Wall  -std=gnu99 -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function 'normData':
sparse_farms.c:191:10: warning: unused variable 'k'
sparse_farms.c:191:6: warning: unused variable 'i'
sparse_farms.c: In function 'sparseFarmsC':
sparse_farms.c:262:41: warning: unused variable 'invpPsi'
sparse_farms.c:259:9: warning: unused variable 'sumhelp'
g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LE:/biocbld/bbs-2.9-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386
** R
** demo
** 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: tools
Loading required package: bit
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


Attaching package: 'bit'

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

    xor

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

- 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

Attaching package ff

Attaching package: 'ff'

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

    write.csv, write.csv2

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

    is.factor, is.ordered

================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: E:/biocbld/bbs-2.9-bioc/tmpdir/RtmpKUKsSg/R.INSTALL7b40f94/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Loading required package: snow
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'cn.farms.Rnw' 
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: E:/biocbld/bbs-2.9-bioc/tmpdir/RtmpKUKsSg/R.INSTALL7b40f94/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Use options(cluster=makeCluster(...))
================================================================================
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.1.2.zip

* DONE (cn.farms)