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Package 114/553HostnameOS / ArchBUILDCHECKBUILD BIN
cn.mops 1.2.6
Guenter Klambauer
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/cn.mops
Last Changed Rev: 67018 / Revision: 69725
Last Changed Date: 2012-06-26 00:27:39 -0700 (Tue, 26 Jun 2012)
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: 1.2.6
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.mops_1.2.6.tar.gz
StartedAt: 2012-09-23 23:46:51 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 23:50:25 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 214.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/cn.mops.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cn.mops/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.mops' version '1.2.6'
* 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 whether package 'cn.mops' 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'bioinf.cls', 'natbib.bst', 'natbib.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/cn.mops.Rcheck/00check.log'
for details.

cn.mops.Rcheck/00install.out:

* installing *source* package 'cn.mops' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c R_init_cnmops.c -o R_init_cnmops.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c cnmops.cpp -o cnmops.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
segment.cpp:65: warning: unused variable 'Rf_beta'
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.10-bioc/meat/cn.mops.Rcheck/cn.mops/libs/i386
** 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
CNVDetectionResult0.0020.0000.003
cn.mops30.089 1.72531.925
cnvr0.7620.0350.801
cnvs0.4890.0180.508
getReadCountsFromBAM0.2610.0340.297
getSegmentReadCountsFromBAM0.1240.0040.129
haplocn.mops2.7960.0642.865
individualCall0.5840.0230.609
iniCall0.5640.0220.588
integerCopyNumber0.5990.0200.621
localAssessments0.5650.0190.585
normalizeChromosomes0.5610.0440.606
normalizeGenome0.5420.0470.590
normalizedData0.5440.0250.573
params0.5030.0260.531
posteriorProbs0.6340.0400.675
segment0.0870.0010.087
segmentation0.5080.0200.529
segplot3.6220.2183.921