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Package 99/467HostnameOS / ArchBUILDCHECKBUILD BIN
cn.farms 1.0.12
Andreas Mitterecker
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/cn.farms
Last Changed Rev: 57324 / Revision: 59457
Last Changed Date: 2011-08-09 09:17:24 -0700 (Tue, 09 Aug 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: cn.farms
Version: 1.0.12
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.farms_1.0.12.tar.gz
StartedAt: 2011-10-20 14:22:59 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:26:06 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 186.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cn.farms.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/cn.farms.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cn.farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.farms' version '1.0.12'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'cn.farms' can be installed ... WARNING
Found the following significant warnings:
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
See '/Users/biocbuild/bbs-2.8-bioc/meat/cn.farms.Rcheck/00install.out' for details.
* 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 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 ... 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

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/cn.farms.Rcheck/00check.log'
for details

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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c R_init_cnfarms.c -o R_init_cnfarms.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:420: warning: unused variable 'method'
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:198: warning: 'I1right' may be used uninitialized in this function
laplace.cpp:197: warning: 'I1left' may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c sparse_farms.c -o sparse_farms.o
sparse_farms.c: In function 'normData':
sparse_farms.c:191: warning: unused variable 'k'
sparse_farms.c:191: warning: unused variable 'i'
sparse_farms.c: In function 'sparseFarmsC':
sparse_farms.c:262: warning: unused variable 'invpPsi'
sparse_farms.c:259: warning: unused variable 'sumhelp'
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-2.8-bioc/meat/cn.farms.Rcheck/cn.farms/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: /Users/biocbuild/bbs-2.8-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(...))
================================================================================

**************************************************************************
   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 ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: /Users/biocbuild/bbs-2.8-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(...))
================================================================================
Warning messages:
1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 

* DONE (cn.farms)

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

nameusersystemelapsed
combineData1.3260.0641.431
createAnnotation000
distributionDistance0.5880.0890.681
dnaCopySf0.2770.0160.293
fragLengCorr6.4690.0476.586
mlSummarization2.6060.1922.833
normalizeAverage0.0020.0010.002
normalizeCels0.0000.0000.001
normalizeNpData000
plotDendrogram0.5590.0870.649
plotDensity1.1230.0811.207
plotEvalIc0.3260.0260.362
plotRegions0.3190.0170.341
plotSmoothScatter0.9090.0771.015
plotViolines0.3360.0170.353
slSummarization2.3740.1182.550
sparseFarmsC0.0010.0000.002
summarizeFarmsExact0.0060.0020.008
summarizeFarmsGaussian0.0050.0010.005
summarizeFarmsMethods0.0040.0000.003
summarizeFarmsVariational0.0060.0010.007
summarizeWindowBps0.0140.0000.014
summarizeWindowMethods0.0050.0000.005
summarizeWindowStd0.0050.0000.006