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CHECK report for ROntoTools on celaya2

This page was generated on 2020-01-16 13:36:48 -0500 (Thu, 16 Jan 2020).

Package 1464/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ROntoTools 2.15.0
Calin Voichita
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/ROntoTools
Branch: master
Last Commit: 4693f26
Last Changed Date: 2019-10-29 13:36:47 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ROntoTools
Version: 2.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ROntoTools_2.15.0.tar.gz
StartedAt: 2020-01-16 08:21:38 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:26:10 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 272.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ROntoTools.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ROntoTools_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ROntoTools.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.15.0’
* 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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plot.peRes-methods     15.711  0.549  16.261
pDis                   12.578  0.597  13.176
peNodeRenderInfo       11.845  0.615  12.463
peEdgeRenderInfo       11.776  0.539  12.317
summary.peRes          11.658  0.546  12.206
pe                     11.423  0.589  12.013
summary.pDisRes        11.398  0.533  11.931
plot.pePathway-methods 10.257  0.524  10.782
* 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-3.11-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.



Installation output

ROntoTools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ROntoTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ROntoTools’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ROntoTools)

Tests output

ROntoTools.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("ROntoTools")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

Using cached pathway data. Database info:
pathway          KEGG Pathway Database
path             Release 73.0+/01-03, Jan 15
                 Kanehisa Laboratories
                 343,170 entries
Default parameters detected. Using pre-parsed data.
Using cached pathway data. Database info:
pathway          KEGG Pathway Database
path             Release 73.0+/01-03, Jan 15
                 Kanehisa Laboratories
                 343,170 entries
Default parameters detected. Using pre-parsed data.
Using cached pathway data. Database info:
pathway          KEGG Pathway Database
path             Release 73.0+/01-03, Jan 15
                 Kanehisa Laboratories
                 343,170 entries
Default parameters detected. Using pre-parsed data.
Performing pathway analysis...

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  |======================================================================| 100%Analysis completed in 7.887847 secs.


RUNIT TEST PROTOCOL -- Thu Jan 16 08:26:02 2020 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ROntoTools RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 21.904   1.527  23.382 

Example timings

ROntoTools.Rcheck/ROntoTools-Ex.timings

nameusersystemelapsed
alpha1MR0.0170.0030.022
alphaMLG0.0170.0010.018
compute.fisher0.0010.0000.001
compute.normalInv0.0010.0010.001
keggPathwayGraphs0.6790.0320.712
keggPathwayNames0.5570.0350.592
nodeWeights0.0100.0000.011
pDis12.578 0.59713.176
pe11.423 0.58912.013
peEdgeRenderInfo11.776 0.53912.317
peNodeRenderInfo11.845 0.61512.463
plot.pePathway-methods10.257 0.52410.782
plot.peRes-methods15.711 0.54916.261
setEdgeWeights3.5610.0683.629
setNodeWeights0.6490.0260.675
summary.pDisRes11.398 0.53311.931
summary.peRes11.658 0.54612.206