BioC 2.12: CHECK report for cn.mops on petty

Package: cn.mops

Version: 1.6.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.mops_1.6.7.tar.gz

StartedAt: 2013-10-08 22:00:55 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:05:35 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 280.6 seconds

RetCode: 0

Status:  OK

CheckDir: cn.mops.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-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 '1.6.7'
* 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 ... [23s/24s] 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 ... NOTE
referencecn.mops: no visible binding for global variable 'input'
* 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' ... OK
* checking examples ... [60s/61s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cn.mops      20.422  0.260  20.821
exomecn.mops  8.437  0.105   8.638
* 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-2.12-bioc/meat/cn.mops.Rcheck/00check.log'
for details.

* installing *source* package 'cn.mops' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c R_init_cnmops.c -o R_init_cnmops.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c cnmops.cpp -o cnmops.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c segment.cpp -o segment.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.12-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
** testing if installed package can be loaded
* DONE (cn.mops)

name	user	system	elapsed
CNVDetectionResult	0.267	0.009	0.275
calcIntegerCopyNumbers	1.387	0.046	1.461
cn.mops	20.422	0.260	20.821
cnvr	0.603	0.029	0.638
cnvs	0.578	0.022	0.604
exomecn.mops	8.437	0.105	8.638
getReadCountsFromBAM	0.419	0.021	0.442
getSegmentReadCountsFromBAM	0.136	0.011	0.148
gr	0.631	0.029	0.679
haplocn.mops	2.739	0.031	2.811
individualCall	0.652	0.018	0.673
iniCall	0.620	0.020	0.642
integerCopyNumber	0.624	0.014	0.646
localAssessments	0.635	0.017	0.660
makeRobustCNVR	0.933	0.025	0.965
normalizeChromosomes	1.221	0.056	1.286
normalizeGenome	0.872	0.048	0.928
normalizedData	0.652	0.031	0.713
params	0.560	0.025	0.605
posteriorProbs	0.549	0.014	0.601
referencecn.mops	2.496	0.025	2.557
sampleNames	0.831	0.019	0.854
segment	0.056	0.005	0.061
segmentation	0.576	0.017	0.593
segplot	2.602	0.026	2.664