BioC 2.13: CHECK report for ddgraph on perceval
This page was generated on 2014-04-05 09:52:51 -0700 (Sat, 05 Apr 2014).
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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ddgraph_1.6.3.tar.gz |
StartedAt: 2014-04-05 00:41:48 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 00:45:48 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 240.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ddgraph.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ddgraph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [13s/13s] 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotPCalg 23.349 0.079 23.525
calcDependence 9.205 0.078 9.293
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘test-all.R’ [107s/108s]
[108s/108s] 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
‘/Users/biocbuild/bbs-2.13-bioc/meat/ddgraph.Rcheck/00check.log’
for details.
ddgraph.Rcheck/00install.out:
* installing *source* package ‘ddgraph’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp: In function ‘SEXPREC* mcX2CLoopC(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
mcX2cloop.cpp:14: warning: label ‘Rcpp’ defined but not used
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ddgraph.so mcX2cloop.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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:
name | user | system | elapsed
|
biased-dot-bn-dot-fit | 0.146 | 0.003 | 0.149 |
|
biased-dot-graph | 0.008 | 0.000 | 0.009 |
|
calcDependence | 9.205 | 0.078 | 9.293 |
|
ciTest-comma-DDDataSet-dash-method | 0.049 | 0.003 | 0.053 |
|
combinationsTest | 0.039 | 0.003 | 0.042 |
|
convertPvalueToColorIndex | 0.008 | 0.000 | 0.009 |
|
convertToFactor | 0.017 | 0.001 | 0.018 |
|
estimateNetworkDistribution | 0.140 | 0.003 | 0.145 |
|
formulaFalseNeg | 0.023 | 0.001 | 0.023 |
|
independent-dot-contributions-dot-formula-dot-mul | 0.013 | 0.001 | 0.014 |
|
independent-dot-contributions-dot-formula | 0.011 | 0.001 | 0.011 |
|
is-dot-binary | 0.012 | 0.000 | 0.013 |
|
logseq | 0.009 | 0.000 | 0.009 |
|
makeDDDataSet | 0.013 | 0.001 | 0.014 |
|
mapEnrichmentToColorsDual | 0.009 | 0.001 | 0.010 |
|
mcMITest | 0.025 | 0.001 | 0.026 |
|
mcX2Test | 0.033 | 0.000 | 0.034 |
|
mcX2TestB50k | 0.423 | 0.009 | 0.441 |
|
mesoBin | 0.013 | 0.003 | 0.015 |
|
mesoCont | 0.014 | 0.002 | 0.016 |
|
ncpc | 3.368 | 0.036 | 3.445 |
|
ncpcResampling | 0.010 | 0.002 | 0.012 |
|
plot-comma-DDGraph-comma-missing-dash-method | 0.011 | 0.002 | 0.017 |
|
plotBNLearn | 0.561 | 0.014 | 0.591 |
|
plotPCalg | 23.349 | 0.079 | 23.525 |
|
prob-dot-distr-dot-norm | 0.009 | 0.003 | 0.012 |
|
prob-dot-distr-dot-unif | 0.008 | 0.001 | 0.009 |
|
random-dot-bn-dot-fit | 0.027 | 0.003 | 0.031 |
|
readFurlongData | 0.040 | 0.022 | 0.062 |
|
recalculateSVMparams | 0.007 | 0.000 | 0.007 |
|
toDDDataSet-comma-FurlongDataSet-dash-method | 0.160 | 0.003 | 0.164 |
|
toyExample | 0.105 | 0.005 | 0.110 |
|