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Package 100/462HostnameOS / ArchBUILDCHECKBUILD BIN
cn.farms 1.1.1
Andreas Mitterecker
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.farms
Last Changed Rev: 55081 / Revision: 55359
Last Changed Date: 2011-04-26 01:41:25 -0700 (Tue, 26 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: cn.farms
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.farms_1.1.1.tar.gz
StartedAt: 2011-05-09 14:02:54 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:06:03 -0700 (Mon, 09 May 2011)
EllapsedTime: 188.7 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.1.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘cn.farms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... 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

cn.farms.Rcheck/00install.out:

* installing *source* package ‘cn.farms’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c R_init_cnfarms.c -o R_init_cnfarms.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c laplace.cpp -o laplace.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c sparse_farms.c -o sparse_farms.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/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")=="/tmp/RtmpCR21Oz"

- 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")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- 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 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/00_pkg_src/cn.farms
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Loading required package: snow

Attaching package: ‘snow’

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

    enquote

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 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: /Users/biocbuild/bbs-2.9-bioc/meat/cn.farms.Rcheck/00_pkg_src/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(...))
================================================================================

* DONE (cn.farms)

cn.farms.Rcheck/cn.farms-Ex.timings:

nameusersystemelapsed
combineData1.1680.0561.263
createAnnotation000
distributionDistance0.7030.0940.805
dnaCopySf0.2750.0150.293
fragLengCorr6.6820.0636.795
mlSummarization2.7360.2082.970
normalizeAverage0.0020.0010.003
normalizeCels000
normalizeNpData0.0010.0010.001
plotDendrogram0.4280.0950.531
plotDensity1.0070.0741.089
plotEvalIc0.3120.0210.353
plotRegions0.3520.0190.371
plotSmoothScatter0.6350.0710.720
plotViolines0.3150.0140.332
slSummarization2.7490.1183.002
sparseFarmsC0.0010.0000.002
summarizeFarmsExact0.0080.0010.009
summarizeFarmsGaussian0.0070.0000.007
summarizeFarmsMethods0.0040.0000.004
summarizeFarmsVariational0.0080.0010.009
summarizeWindowBps0.0140.0000.017
summarizeWindowMethods0.0040.0000.004
summarizeWindowStd0.0070.0010.007