BioC 3.3: CHECK report for ddgraph on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:08 -0400 (Tue, 27 Oct 2015).
ddgraph 1.15.0
Robert Stojnic
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ddgraph | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
Summary
| Package: ddgraph |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.15.0.tar.gz |
| StartedAt: 2015-10-27 03:13:26 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 03:15:23 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 117.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ddgraph.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ddgraph.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-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 ‘1.15.0’
* 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 ... [7s/7s] 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
'library' or 'require' call to ‘Rgraphviz’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
customPlotPCAlgo: no visible global function definition for
‘layoutGraph’
customPlotPCAlgo: no visible global function definition for
‘renderGraph’
plotSVMPerformance: no visible global function definition for
‘prediction’
plotSVMPerformance: no visible global function definition for
‘performance’
recalculateSVMparams: no visible global function definition for ‘svm’
recalculateSVMparams : <anonymous>: no visible global function
definition for ‘svm’
recalculateSVMparams: no visible global function definition for
‘prediction’
recalculateSVMparams: no visible global function definition for
‘performance’
svmFeatureSelectionLOOCV: no visible global function definition for
‘svm’
plot,DDGraph-missing: no visible global function definition for
‘layoutGraph’
plot,DDGraph-missing: no visible global function definition for
‘renderGraph’
Undefined global functions or variables:
layoutGraph performance prediction renderGraph svm
* 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 GNU extensions in Makefiles ... 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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotPCalg 12.648 0.008 12.676
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [53s/53s]
[53s/53s] 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
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/ddgraph.Rcheck/00check.log’
for details.
ddgraph.Rcheck/00install.out:
* installing *source* package ‘ddgraph’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -fpic -g -O2 -c mcX2cloop.cpp -o mcX2cloop.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o ddgraph.so mcX2cloop.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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 | 0.007 | 0.000 | 0.010 |
|
| biased-dot-graph | 0.004 | 0.001 | 0.003 |
|
| calcDependence | 3.720 | 0.011 | 3.734 |
|
| ciTest-comma-DDDataSet-dash-method | 0.017 | 0.000 | 0.017 |
|
| combinationsTest | 0.016 | 0.000 | 0.016 |
|
| convertPvalueToColorIndex | 0 | 0 | 0 |
|
| convertToFactor | 0.004 | 0.000 | 0.004 |
|
| estimateNetworkDistribution | 0.065 | 0.000 | 0.065 |
|
| formulaFalseNeg | 0.003 | 0.000 | 0.002 |
|
| independent-dot-contributions-dot-formula-dot-mul | 0.002 | 0.000 | 0.001 |
|
| independent-dot-contributions-dot-formula | 0.001 | 0.000 | 0.001 |
|
| is-dot-binary | 0.001 | 0.000 | 0.001 |
|
| logseq | 0.000 | 0.000 | 0.001 |
|
| makeDDDataSet | 0.001 | 0.000 | 0.002 |
|
| mapEnrichmentToColorsDual | 0.001 | 0.000 | 0.000 |
|
| mcMITest | 0.006 | 0.000 | 0.006 |
|
| mcX2Test | 0.009 | 0.000 | 0.009 |
|
| mcX2TestB50k | 0.263 | 0.004 | 0.267 |
|
| mesoBin | 0.002 | 0.000 | 0.003 |
|
| mesoCont | 0.000 | 0.000 | 0.002 |
|
| ncpc | 1.215 | 0.008 | 1.225 |
|
| ncpcResampling | 0 | 0 | 0 |
|
| plot-comma-DDGraph-comma-missing-dash-method | 0 | 0 | 0 |
|
| plotBNLearn | 0.191 | 0.008 | 0.199 |
|
| plotPCalg | 12.648 | 0.008 | 12.676 |
|
| prob-dot-distr-dot-norm | 0.000 | 0.000 | 0.001 |
|
| prob-dot-distr-dot-unif | 0.000 | 0.000 | 0.001 |
|
| random-dot-bn-dot-fit | 0.003 | 0.000 | 0.003 |
|
| readFurlongData | 0.014 | 0.008 | 0.023 |
|
| recalculateSVMparams | 0.001 | 0.000 | 0.000 |
|
| toDDDataSet-comma-FurlongDataSet-dash-method | 0.069 | 0.000 | 0.068 |
|
| toyExample | 0.131 | 0.000 | 0.131 |
|