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BioC 2.13: CHECK report for ddgraph on zin1

This page was generated on 2014-04-05 09:48:18 -0700 (Sat, 05 Apr 2014).

Package 191/750HostnameOS / ArchBUILDCHECKBUILD BIN
ddgraph 1.6.3
Robert Stojnic
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ddgraph
Last Changed Rev: 87517 / Revision: 88450
Last Changed Date: 2014-03-17 10:58:58 -0700 (Mon, 17 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ddgraph
Version: 1.6.3
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.6.3.tar.gz
StartedAt: 2014-04-05 00:39:39 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:42:10 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 151.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ddgraph.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ddgraph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.6.3’
* 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rcpp’ ‘testthat’
A package should be listed in only one of these fields.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ddgraph.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      17.733  0.016  17.779
calcDependence  6.728  0.048   6.794
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [70s/70s]
 [70s/70s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/ddgraph.Rcheck/00check.log’
for details.

ddgraph.Rcheck/00install.out:

* installing *source* package ‘ddgraph’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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-fit0.0680.0040.074
biased-dot-graph0.0040.0000.005
calcDependence6.7280.0486.794
ciTest-comma-DDDataSet-dash-method0.1080.0040.110
combinationsTest0.0240.0040.026
convertPvalueToColorIndex0.0040.0000.004
convertToFactor0.0080.0000.008
estimateNetworkDistribution0.0920.0040.096
formulaFalseNeg0.0040.0000.004
independent-dot-contributions-dot-formula-dot-mul0.0040.0000.004
independent-dot-contributions-dot-formula0.0040.0000.004
is-dot-binary0.0040.0000.003
logseq0.0040.0000.003
makeDDDataSet0.0040.0000.006
mapEnrichmentToColorsDual0.0040.0000.002
mcMITest0.0120.0000.012
mcX2Test0.0120.0000.013
mcX2TestB50k0.3640.0040.366
mesoBin0.0040.0040.005
mesoCont0.0080.0000.005
ncpc1.9320.0441.979
ncpcResampling0.0040.0000.003
plot-comma-DDGraph-comma-missing-dash-method0.0040.0000.002
plotBNLearn0.3320.0000.332
plotPCalg17.733 0.01617.779
prob-dot-distr-dot-norm0.0000.0000.002
prob-dot-distr-dot-unif0.0040.0000.002
random-dot-bn-dot-fit0.0040.0000.005
readFurlongData0.0200.0080.030
recalculateSVMparams0.0040.0000.001
toDDDataSet-comma-FurlongDataSet-dash-method0.0880.0040.091
toyExample0.0640.0000.066