MLP 1.24.0
Tobias Verbeke
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MLP | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf MLP.buildbin-libdir MLP.Rcheck && mkdir MLP.buildbin-libdir MLP.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLP.buildbin-libdir MLP_1.24.0.tar.gz >MLP.Rcheck\00install.out 2>&1 && cp MLP.Rcheck\00install.out MLP-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MLP.buildbin-libdir --install="check:MLP-install.out" --force-multiarch --no-vignettes --timings MLP_1.24.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MLP.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MLP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MLP' version '1.24.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 'title'
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 'edges'
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<- edges getGOTerm graphRenderInfo
graphRenderInfo<- layoutGraph legend lookUp lsfit matlines 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 title
Consider adding
importFrom("graphics", "axis", "barplot", "legend", "matlines", "par",
"plot", "points", "text", "title")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MLP 22.03 0.56 22.59
getGeneSets 19.35 1.31 88.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MLP 25.84 0.59 26.44
getGeneSets 16.86 0.88 17.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.MLP.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/MLP.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'MLP' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'MLP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLP' as MLP_1.24.0.zip
* DONE (MLP)