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BioC 2.14: CHECK report for DirichletMultinomial on zin2

This page was generated on 2014-10-08 08:49:30 -0700 (Wed, 08 Oct 2014).

Package 228/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DirichletMultinomial 1.6.0
Martin Morgan
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/DirichletMultinomial
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: DirichletMultinomial
Version: 1.6.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings DirichletMultinomial_1.6.0.tar.gz
StartedAt: 2014-10-07 23:11:12 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:12:04 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 51.4 seconds
RetCode: 0
Status:  OK 
CheckDir: DirichletMultinomial.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings DirichletMultinomial_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/DirichletMultinomial.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DirichletMultinomial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DirichletMultinomial’ version ‘1.6.0’
* 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 ‘DirichletMultinomial’ 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 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* 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

DirichletMultinomial.Rcheck/00install.out:

* installing *source* package ‘DirichletMultinomial’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c dirichlet_fit.c -o dirichlet_fit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fpic  -g -O2  -Wall -c dirichlet_fit_main.c -o dirichlet_fit_main.o
dirichlet_fit_main.c: In function ‘dirichlet_fit_main’:
dirichlet_fit_main.c:542:17: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o DirichletMultinomial.so R_init_DirichletMultinomial.o dirichlet_fit.o dirichlet_fit_main.o -L/usr/lib -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/DirichletMultinomial.Rcheck/DirichletMultinomial/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 (DirichletMultinomial)

DirichletMultinomial.Rcheck/DirichletMultinomial-Ex.timings:

nameusersystemelapsed
DMN-class0.0160.0080.024
DMNGroup-class0.0120.0000.012
cvdmngroup0.0040.0000.005
dataobjects0.0160.0000.016
dmn0.0040.0000.007
dmngroup0.0080.0000.007
fitted0.2080.0000.208
heatmapdmn0.0720.0000.103
roc0.2520.0080.259
util0.1160.0000.117