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BioC 3.0: CHECK report for birta on zin1

This page was generated on 2015-04-10 09:39:48 -0700 (Fri, 10 Apr 2015).

Package 105/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birta 1.10.0
Benedikt Zacher , Holger Froehlich
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/birta
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: birta
Version: 1.10.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings birta_1.10.0.tar.gz
StartedAt: 2015-04-09 22:03:56 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:04:38 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 42.5 seconds
RetCode: 0
Status:  OK 
CheckDir: birta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings birta_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/birta.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘birta/DESCRIPTION’ ... OK
* this is package ‘birta’ 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 ‘birta’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
birta,ExpressionSet-ExpressionSet-ExpressionSet: no visible global
  function definition for ‘exprs’
birta,ExpressionSet-ExpressionSet-missing: no visible global function
  definition for ‘exprs’
birta,ExpressionSet-missing-ExpressionSet: no visible global function
  definition for ‘exprs’
birta,ExpressionSet-missing-missing: no visible global function
  definition for ‘exprs’
limmaAnalysis,ExpressionSet-matrix-character: no visible global
  function definition for ‘exprs’
* 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 compiled code ... NOTE
File ‘birta/libs/birta.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘BayesNetwork.o’, ‘BayesNetworkNC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘BayesNetwork.o’, ‘BayesNetworkNC.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/birta.Rcheck/00check.log’
for details.

birta.Rcheck/00install.out:

* installing *source* package ‘birta’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BayesNetwork.cpp -o BayesNetwork.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BayesNetworkNC.cpp -o BayesNetworkNC.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c getStates.cpp -o getStates.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o birta.so BayesNetwork.o BayesNetworkNC.o getStates.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/birta.Rcheck/birta/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
* DONE (birta)

birta.Rcheck/birta-Ex.timings:

nameusersystemelapsed
birta.run0.8160.0000.817
get_potential_swaps0.0040.0000.002
limmaAnalysis0.1120.0000.110
plotConvergence0.9600.0040.992