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BioC 2.14: CHECK report for ddgraph on zin2

This page was generated on 2014-10-08 08:49:31 -0700 (Wed, 08 Oct 2014).

Package 213/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddgraph 1.8.0
Robert Stojnic
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/ddgraph
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  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ddgraph
Version: 1.8.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.8.0.tar.gz
StartedAt: 2014-10-07 23:04:46 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:07:00 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 134.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ddgraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ddgraph.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 ‘ddgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ddgraph’ version ‘1.8.0’
* 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 ‘ddgraph’ can be installed ... [9s/9s] 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 ... 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 ... [29s/30s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      18.397  0.004  18.474
calcDependence  6.632  0.016   6.660
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [52s/52s]
 [52s/52s] 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

ddgraph.Rcheck/00install.out:

* installing *source* package ‘ddgraph’ ...
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp: In function ‘SEXPREC* mcX2CLoopC(SEXP, SEXP, SEXP, SEXP)’:
mcX2cloop.cpp:14:2: warning: label ‘Rcpp’ defined but not used [-Wunused-label]
g++ -shared -L/usr/local/lib -o ddgraph.so mcX2cloop.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/ddgraph.Rcheck/ddgraph/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 (ddgraph)

ddgraph.Rcheck/ddgraph-Ex.timings:

nameusersystemelapsed
biased-dot-bn-dot-fit0.0160.0000.029
biased-dot-graph0.0640.0000.068
calcDependence6.6320.0166.660
ciTest-comma-DDDataSet-dash-method0.0240.0000.023
combinationsTest0.0240.0000.023
convertPvalueToColorIndex0.0000.0000.001
convertToFactor0.0080.0000.005
estimateNetworkDistribution0.0760.0000.077
formulaFalseNeg0.0000.0000.001
independent-dot-contributions-dot-formula-dot-mul0.0040.0000.002
independent-dot-contributions-dot-formula0.0000.0000.002
is-dot-binary0.0040.0000.001
logseq0.0000.0000.001
makeDDDataSet0.0040.0000.002
mapEnrichmentToColorsDual000
mcMITest0.0080.0000.008
mcX2Test0.0080.0000.010
mcX2TestB50k0.2760.0040.283
mesoBin0.0040.0000.003
mesoCont0.0040.0000.003
ncpc1.8680.0041.875
ncpcResampling0.0000.0000.001
plot-comma-DDGraph-comma-missing-dash-method0.0000.0000.001
plotBNLearn0.2720.0040.278
plotPCalg18.397 0.00418.474
prob-dot-distr-dot-norm000
prob-dot-distr-dot-unif0.0040.0000.001
random-dot-bn-dot-fit0.0040.0000.004
readFurlongData0.0240.0120.034
recalculateSVMparams0.0000.0000.001
toDDDataSet-comma-FurlongDataSet-dash-method0.0960.0040.098
toyExample0.0680.0000.068