ROntoTools 2.4.0
Calin Voichita
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/ROntoTools | | Branch: RELEASE_3_5 | | Last Commit: 5fbd3d8 | | Last Changed Date: 2017-04-24 15:45:44 -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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ROntoTools_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ROntoTools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ROntoTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ROntoTools’ version ‘2.4.0’
* 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 ‘ROntoTools’ can be installed ... 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘ROntoTools’ for: ‘Summary’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Rgraphviz’ ‘methods’
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
KEGGpathway2Graph: no visible global function definition for ‘is’
KEGGpathway2Graph: no visible global function definition for ‘new’
compute.B: no visible global function definition for ‘as’
compute.B_pDis: no visible global function definition for ‘as’
compute.normalInv: no visible global function definition for ‘pnorm’
compute.normalInv: no visible binding for global variable ‘qnorm’
compute.pORA: no visible global function definition for ‘phyper’
get.totalAccNorm: no visible global function definition for ‘sd’
get.totalPertNorm: no visible global function definition for ‘sd’
get.totalpDisNorm: no visible global function definition for ‘sd’
graph2ftM: no visible global function definition for ‘as’
keggPathwayGraphs: no visible global function definition for
‘txtProgressBar’
keggPathwayGraphs : <anonymous>: no visible global function definition
for ‘new’
keggPathwayGraphs : <anonymous>: no visible global function definition
for ‘setTxtProgressBar’
keggPathwayGraphs : <anonymous>: no visible global function definition
for ‘getTxtProgressBar’
loadKEGGpathwayDataREST: no visible global function definition for
‘txtProgressBar’
loadKEGGpathwayDataREST : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
loadKEGGpathwayDataREST : <anonymous>: no visible global function
definition for ‘getTxtProgressBar’
pDis.boot: no visible global function definition for ‘new’
pDis.helper: no visible global function definition for ‘txtProgressBar’
pDis.helper : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
pDis.helper : <anonymous>: no visible global function definition for
‘getTxtProgressBar’
pDis.helper: no visible global function definition for ‘new’
pe.boot: no visible global function definition for ‘new’
peEdgeRenderInfo: no visible global function definition for
‘removedEdges’
peNodeRenderInfo: no visible global function definition for ‘slot’
peNodeRenderInfo: no visible global function definition for
‘colorRampPalette’
pf.helper: no visible global function definition for ‘txtProgressBar’
pf.helper : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
pf.helper : <anonymous>: no visible global function definition for
‘getTxtProgressBar’
pf.helper: no visible global function definition for ‘new’
subGraphByNodeType: no visible global function definition for ‘new’
summary.pDisRes : <anonymous>: no visible global function definition
for ‘p.adjust’
summary.peRes : <anonymous>: no visible global function definition for
‘p.adjust’
plot,pePathway-character: no visible global function definition for
‘slot’
plot,pePathway-character: no visible global function definition for
‘abline’
plot,pePathway-character: no visible global function definition for
‘points’
plot,pePathway-character: no visible global function definition for
‘sd’
plot,pePathway-character: no visible global function definition for
‘density’
plot,peRes-character: no visible global function definition for
‘Summary’
plot,peRes-character: no visible global function definition for ‘chull’
plot,peRes-character: no visible global function definition for
‘polygon’
plot,peRes-character: no visible global function definition for
‘points’
plot,peRes-character: no visible global function definition for ‘text’
plot,peRes-character: no visible global function definition for
‘abline’
Undefined global functions or variables:
Summary abline as chull colorRampPalette density getTxtProgressBar is
new p.adjust phyper pnorm points polygon qnorm removedEdges sd
setTxtProgressBar slot text txtProgressBar
Consider adding
importFrom("grDevices", "chull", "colorRampPalette")
importFrom("graphics", "abline", "points", "polygon", "text")
importFrom("methods", "Summary", "as", "is", "new", "slot")
importFrom("stats", "density", "p.adjust", "phyper", "pnorm", "qnorm",
"sd")
importFrom("utils", "getTxtProgressBar", "setTxtProgressBar",
"txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.pDisRes':
‘summary.pDisRes’
S3 methods shown with full name in documentation object 'summary.peRes':
‘summary.peRes’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
plot.peRes-methods 10.925 0.230 11.500
peNodeRenderInfo 8.231 0.235 8.713
peEdgeRenderInfo 8.129 0.206 8.614
pDis 7.813 0.156 8.172
plot.pePathway-methods 7.533 0.228 8.022
summary.peRes 7.516 0.225 7.974
pe 7.393 0.207 7.840
summary.pDisRes 7.284 0.144 7.658
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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
‘/Users/biocbuild/bbs-3.5-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.