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Package 126/631HostnameOS / ArchBUILDCHECKBUILD BIN
cn.mops 1.5.5
Guenter Klambauer
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.mops
Last Changed Rev: 72181 / Revision: 72575
Last Changed Date: 2012-12-27 02:57:03 -0800 (Thu, 27 Dec 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.mops
Version: 1.5.5
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.5.5.tar.gz
StartedAt: 2013-01-16 01:41:50 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 01:45:17 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 206.7 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/cn.mops.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.mops/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.mops’ version ‘1.5.5’
* 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.mops’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
cn.mops      26.830  0.440  27.274
exomecn.mops  9.244  0.168   9.422
* 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.mops.Rcheck/00install.out:

* installing *source* package ‘cn.mops’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c segment.cpp -o segment.o
g++ -shared -L/usr/local/lib64 -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘cn.mops’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘cn.mops.Rnw’ 
** testing if installed package can be loaded

* DONE (cn.mops)

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

nameusersystemelapsed
CNVDetectionResult0.2760.0080.283
cn.mops26.830 0.44027.274
cnvr0.4520.0000.452
cnvs0.4360.0040.441
exomecn.mops9.2440.1689.422
getReadCountsFromBAM0.3040.0120.317
getSegmentReadCountsFromBAM0.1160.0080.123
gr0.4600.0040.463
haplocn.mops2.4480.0122.457
individualCall0.4680.0040.478
iniCall0.4810.0080.486
integerCopyNumber0.8280.0080.838
localAssessments0.4760.0080.484
normalizeChromosomes0.5680.0000.569
normalizeGenome0.5640.0080.573
normalizedData0.4440.0160.459
params0.4160.0080.424
posteriorProbs0.4120.0040.417
sampleNames0.4080.0080.415
segment0.0560.0000.054
segmentation0.4520.0080.459
segplot2.4320.0242.461