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BioC 2.12: CHECK report for cn.mops on petty

This page was generated on 2013-10-09 09:40:06 -0700 (Wed, 09 Oct 2013).

Package 134/671HostnameOS / ArchBUILDCHECKBUILD BIN
cn.mops 1.6.7
Guenter Klambauer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/cn.mops
Last Changed Rev: 81146 / Revision: 81334
Last Changed Date: 2013-10-03 23:56:20 -0700 (Thu, 03 Oct 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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

Command output

* 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.

cn.mops.Rcheck/00install.out:

* 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)

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

nameusersystemelapsed
CNVDetectionResult0.2670.0090.275
calcIntegerCopyNumbers1.3870.0461.461
cn.mops20.422 0.26020.821
cnvr0.6030.0290.638
cnvs0.5780.0220.604
exomecn.mops8.4370.1058.638
getReadCountsFromBAM0.4190.0210.442
getSegmentReadCountsFromBAM0.1360.0110.148
gr0.6310.0290.679
haplocn.mops2.7390.0312.811
individualCall0.6520.0180.673
iniCall0.6200.0200.642
integerCopyNumber0.6240.0140.646
localAssessments0.6350.0170.660
makeRobustCNVR0.9330.0250.965
normalizeChromosomes1.2210.0561.286
normalizeGenome0.8720.0480.928
normalizedData0.6520.0310.713
params0.5600.0250.605
posteriorProbs0.5490.0140.601
referencecn.mops2.4960.0252.557
sampleNames0.8310.0190.854
segment0.0560.0050.061
segmentation0.5760.0170.593
segplot2.6020.0262.664