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BioC 2.12: CHECK report for biomvRCNS on petty

This page was generated on 2013-10-09 09:40:19 -0700 (Wed, 09 Oct 2013).

Package 78/671HostnameOS / ArchBUILDCHECKBUILD BIN
biomvRCNS 1.0.6
Yang Du
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/biomvRCNS
Last Changed Rev: 79751 / Revision: 81334
Last Changed Date: 2013-08-23 01:39:26 -0700 (Fri, 23 Aug 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: biomvRCNS
Version: 1.0.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biomvRCNS_1.0.6.tar.gz
StartedAt: 2013-10-08 21:44:18 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:51:22 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 424.0 seconds
RetCode: 0
Status:  OK 
CheckDir: biomvRCNS.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/biomvRCNS.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 'biomvRCNS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biomvRCNS' version '1.0.6'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'biomvRCNS' can be installed ... [37s/38s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [52s/54s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
biomvRhsmm 18.868  0.197  19.326
biomvRseg   9.059  0.035   9.496
* 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

biomvRCNS.Rcheck/00install.out:

* installing *source* package 'biomvRCNS' ...
** 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 biomvRCNS.c -o biomvRCNS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o biomvRCNS.so biomvRCNS.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/biomvRCNS.Rcheck/biomvRCNS/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'biomvRCNS'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomvRCNS)

biomvRCNS.Rcheck/biomvRCNS-Ex.timings:

nameusersystemelapsed
biomvRCNS-class0.0080.0020.010
biomvRGviz2.4550.0352.507
biomvRhsmm18.868 0.19719.326
biomvRmgmr1.2600.0111.275
biomvRseg9.0590.0359.496
hsmmRun0.2400.0090.264
maxGapminRun0.0190.0030.021
regionSegAlphaNB0.5800.0040.588
regionSegCost0.0170.0030.019
simSegData0.0140.0050.018
sojournAnno0.1280.0060.135
splitFarNeighbour0.0100.0030.012