BioC 2.12: CHECK report for Mulcom on george2

Package: Mulcom

Version: 1.10.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Mulcom_1.10.0.tar.gz

StartedAt: 2013-10-09 03:34:11 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:36:53 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 161.8 seconds

RetCode: 0

Status:  OK

CheckDir: Mulcom.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Mulcom.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mulcom/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mulcom’ version ‘1.10.0’
* 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 ... [12s/16s] 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NB: .First.lib is obsolete and will not be used in R 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [63s/64s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
mulInt 22.554  0.396  23.380
mulOpt 16.261  0.068  16.508
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/Mulcom.Rcheck/00check.log’
for details.

* installing *source* package ‘Mulcom’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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:708:33: warning: statement has no effect [-Wunused-value]
mulLibs.cc: In function ‘void Complete_SimulationC(double*, int*, double*, double*, int*, int*, int*, int*, int*)’:
mulLibs.cc:1022:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mulLibs.cc:1023:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -shared -L/usr/local/lib -o Mulcom.so mulLibs.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/Mulcom.Rcheck/Mulcom/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package ‘Mulcom’
* DONE (Mulcom)

name	user	system	elapsed
MULCOM-class	1.292	0.012	1.304
MULCOM_P	0.840	0.012	0.877
mulCAND	3.432	0.068	3.503
mulCalc	0.612	0.012	0.631
mulDELTA	0.280	0.016	0.303
mulDiff	1.516	0.052	1.571
mulFSG	2.316	0.044	2.372
mulIndex	0.272	0.004	0.275
mulInt	22.554	0.396	23.380
mulOpt	16.261	0.068	16.508
mulOptPars	1.184	0.016	1.203
mulOptPlot	3.244	0.092	3.340
mulParOpt	2.812	0.036	2.963
mulPerm	1.164	0.012	1.174
mulPermC	0.212	0.008	0.222
mulScores	0.324	0.008	0.330