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BioC 2.12: CHECK report for Mulcom on george2

This page was generated on 2013-10-09 09:37:39 -0700 (Wed, 09 Oct 2013).

Package 430/671HostnameOS / ArchBUILDCHECKBUILD BIN
Mulcom 1.10.0
Claudio Isella
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/Mulcom
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

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

Command output

* 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.

Mulcom.Rcheck/00install.out:

* 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)

Mulcom.Rcheck/Mulcom-Ex.timings:

nameusersystemelapsed
MULCOM-class1.2920.0121.304
MULCOM_P0.8400.0120.877
mulCAND3.4320.0683.503
mulCalc0.6120.0120.631
mulDELTA0.2800.0160.303
mulDiff1.5160.0521.571
mulFSG2.3160.0442.372
mulIndex0.2720.0040.275
mulInt22.554 0.39623.380
mulOpt16.261 0.06816.508
mulOptPars1.1840.0161.203
mulOptPlot3.2440.0923.340
mulParOpt2.8120.0362.963
mulPerm1.1640.0121.174
mulPermC0.2120.0080.222
mulScores0.3240.0080.330