Package: Mulcom

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Mulcom_1.9.1.tar.gz

StartedAt: 2013-03-25 03:43:16 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:45:37 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 141.3 seconds

RetCode: 0

Status:  OK

CheckDir: Mulcom.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Mulcom.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Mulcom/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Mulcom' version '1.9.1'
* 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 'Mulcom' can be installed ... [10s/10s] 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'Mulcom/R/mulib.R':
  .First.lib calls:
    cat("Mulcom loaded\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
* 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 ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
mulInt 15.052  5.527  20.811
mulOpt 11.301  3.913  15.366
* 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/Mulcom.Rcheck/00check.log'
for details.

* installing *source* package 'Mulcom' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c mulLibs.cc -o mulLibs.o
mulLibs.cc: In function 'void Single_SimulationC(double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*)':
mulLibs.cc:708: warning: statement has no effect
mulLibs.cc: In function 'void Complete_SimulationC(double*, int*, double*, double*, int*, int*, int*, int*, int*)':
mulLibs.cc:1022: warning: comparison between signed and unsigned integer expressions
mulLibs.cc:1023: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Mulcom.so mulLibs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Mulcom.Rcheck/Mulcom/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MulcomVignette.Rnw' 
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package 'Mulcom'
* DONE (Mulcom)

name	user	system	elapsed
MULCOM-class	1.158	0.056	1.216
MULCOM_P	0.819	0.043	0.863
mulCAND	3.626	0.137	3.768
mulCalc	0.721	0.048	0.773
mulDELTA	0.436	0.024	0.460
mulDiff	2.594	0.119	2.720
mulFSG	2.500	0.146	2.650
mulIndex	0.333	0.016	0.348
mulInt	15.052	5.527	20.811
mulOpt	11.301	3.913	15.366
mulOptPars	1.939	0.090	2.031
mulOptPlot	3.635	0.609	4.272
mulParOpt	3.469	0.659	4.150
mulPerm	1.903	0.099	2.003
mulPermC	0.281	0.015	0.297
mulScores	0.551	0.039	0.590