MLP 1.16.0
Tobias Verbeke
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/MLP | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLP_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/MLP.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLP’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘AnnotationDbi’ ‘affy’ ‘plotrix’ ‘gplots’ ‘gmodels’ ‘gdata’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘MLP’ can be installed ... [13s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘annotate’ ‘GO.db’ ‘GOstats’ ‘KEGG.db’ ‘org.Cf.eg.db’ ‘org.Hs.eg.db’
‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘reactome.db’ ‘Rgraphviz’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘affy’ ‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’ ‘plotrix’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGeneSetDescription: no visible binding for global variable ‘GOTERM’
addGeneSetDescription: no visible binding for global variable
‘KEGGPATHID2NAME’
addGeneSetDescription: no visible binding for global variable
‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
‘org.Mm.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
‘org.Hs.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
‘org.Rn.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
‘org.Cf.egGO2ALLEGS’
getGeneSets: no visible binding for global variable ‘GOBPANCESTOR’
getGeneSets: no visible binding for global variable ‘GOMFANCESTOR’
getGeneSets: no visible binding for global variable ‘GOCCANCESTOR’
getGeneSets: no visible binding for global variable ‘GOTERM’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2EXTID’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2NAME’
getGeneSets: no visible binding for global variable
‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
‘reactomePATHID2EXTID’
plotGeneSetSignificance: no visible global function definition for
‘lookUp’
plotGOgraph: no visible global function definition for ‘GOGraph’
plotGOgraph: no visible global function definition for ‘removeNode’
plotGOgraph: no visible global function definition for ‘nodes’
plotGOgraph: no visible global function definition for ‘layoutGraph’
plotGOgraph: no visible global function definition for ‘colorpanel’
plotGOgraph: no visible global function definition for
‘nodeRenderInfo<-’
plotGOgraph: no visible global function definition for ‘getGOTerm’
plotGOgraph: no visible global function definition for ‘edgeRenderInfo’
plotGOgraph: no visible global function definition for
‘edgeRenderInfo<-’
plotGOgraph: no visible global function definition for
‘graphRenderInfo’
plotGOgraph: no visible global function definition for
‘graphRenderInfo<-’
plotGOgraph: no visible global function definition for ‘renderGraph’
plotGOgraph: no visible global function definition for ‘smartlegend’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [103s/109s] WARNING
Found the following significant warnings:
Warning: 'smartlegend' is deprecated.
Warning: 'smartlegend' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
MLP 47.532 5.464 53.062
getGeneSets 29.838 3.674 38.948
plot.MLP 6.261 0.126 6.668
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.MLP.R’ [103s/104s]
[104s/104s] 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: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/MLP.Rcheck/00check.log’
for details.
* installing *source* package ‘MLP’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (MLP)