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Package 125/631HostnameOS / ArchBUILDCHECKBUILD BIN
cn.farms 1.7.1
Andreas Mitterecker
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.farms
Last Changed Rev: 71026 / Revision: 72575
Last Changed Date: 2012-11-07 09:19:29 -0800 (Wed, 07 Nov 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: cn.farms
Version: 1.7.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.7.1.tar.gz
StartedAt: 2013-01-16 01:41:02 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 01:44:30 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 207.9 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘1.7.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cn.farms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mlSummarization 5.085  0.132   5.216
* 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c laplace.cpp -o laplace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/usr/local/lib64 -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘cn.farms.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (cn.farms)

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

nameusersystemelapsed
combineData1.8160.0241.841
createAnnotation0.0080.0000.010
distributionDistance0.5280.0040.531
dnaCopySf0.1640.0040.168
fragLengCorr3.9200.0083.934
mlSummarization5.0850.1325.216
normalizeAverage0.0080.0000.009
normalizeCels0.0040.0040.008
normalizeNpData0.0080.0040.012
plotDendrogram0.5040.0040.511
plotDensity0.6040.0080.611
plotEvalIc0.7280.0160.781
plotRegions0.180.000.18
plotSmoothScatter0.3560.0200.374
plotViolines0.1840.0000.185
slSummarization4.5240.0324.558
sparseFarmsC0.0080.0000.007
summarizeFarmsExact0.0120.0000.014
summarizeFarmsExact20.0120.0040.014
summarizeFarmsExact30.0200.0000.019
summarizeFarmsGaussian0.0160.0000.016
summarizeFarmsMethods0.0080.0000.006
summarizeFarmsVariational0.0160.0000.013
summarizeWindowBps0.0240.0000.025
summarizeWindowMethods0.0160.0000.017
summarizeWindowStd0.0160.0000.016