MLP 1.20.0
Tobias Verbeke
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/MLP | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MLP_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MLP.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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 ... 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:
‘GO.db’ ‘GOstats’ ‘KEGG.db’ ‘Rgraphviz’ ‘annotate’ ‘org.Cf.eg.db’
‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘reactome.db’
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
MLP: no visible global function definition for ‘na.omit’
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’
mlpBarplot: no visible global function definition for ‘par’
mlpBarplot: no visible global function definition for ‘barplot’
mlpBarplot: no visible global function definition for ‘mtext’
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 ‘legend’
plotGeneSetSignificance: no visible global function definition for
‘lookUp’
plotGeneSetSignificance: no visible global function definition for
‘barplot’
plotQuantileCurves: no visible global function definition for ‘plot’
plotQuantileCurves: no visible global function definition for ‘axis’
plotQuantileCurves: no visible global function definition for ‘par’
plotQuantileCurves: no visible global function definition for ‘points’
plotQuantileCurves: no visible global function definition for ‘text’
plotQuantileCurves: no visible global function definition for
‘matlines’
quantileCurves: no visible binding for global variable ‘quantile’
quantileCurves: no visible global function definition for ‘predict’
quantileCurves: no visible global function definition for
‘smooth.spline’
quantileCurves : tt: no visible global function definition for
‘smooth.spline’
quantileCurves : tt: no visible global function definition for
‘predict’
quantileCurves : tt: no visible global function definition for
‘quantile’
quantileCurves : vv: no visible global function definition for
‘smooth.spline’
quantileCurves : vv: no visible global function definition for
‘quantile’
quantileCurves : vv: no visible global function definition for
‘predict’
smdecreasing1: no visible global function definition for ‘approx’
smdecreasing1: no visible global function definition for ‘lsfit’
Undefined global functions or variables:
GOBPANCESTOR GOCCANCESTOR GOGraph GOMFANCESTOR GOTERM
KEGGPATHID2EXTID KEGGPATHID2NAME approx axis barplot colorpanel
edgeRenderInfo edgeRenderInfo<- getGOTerm graphRenderInfo
graphRenderInfo<- layoutGraph legend lookUp lsfit matlines mtext
na.omit nodeRenderInfo<- nodes org.Cf.egGO2ALLEGS org.Hs.egGO2ALLEGS
org.Mm.egGO2ALLEGS org.Rn.egGO2ALLEGS par plot points predict
quantile reactomePATHID2EXTID reactomePATHNAME2ID removeNode
renderGraph smooth.spline text
Consider adding
importFrom("graphics", "axis", "barplot", "legend", "matlines",
"mtext", "par", "plot", "points", "text")
importFrom("stats", "approx", "lsfit", "na.omit", "predict",
"quantile", "smooth.spline")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MLP 24.761 0.141 24.898
getGeneSets 17.027 0.291 17.585
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.MLP.R’
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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/MLP.Rcheck/00check.log’
for details.