Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-06-17 02:39:22 -0400 (Thu, 17 Jun 2021).

CHECK results for ROntoTools on machv2

To the developers/maintainers of the ROntoTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ROntoTools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1620/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ROntoTools 2.20.0  (landing page)
Calin Voichita
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/ROntoTools
Branch: RELEASE_3_13
Last Commit: b1691c3
Last Changed Date: 2021-05-19 11:58:19 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ROntoTools
Version: 2.20.0
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_2.20.0.tar.gz
StartedAt: 2021-06-15 23:12:11 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 23:15:36 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 205.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ROntoTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ROntoTools.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.20.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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     12.696  0.112  12.823
peNodeRenderInfo        9.889  0.132  10.035
plot.pePathway-methods  9.341  0.130   9.539
summary.pDisRes         9.097  0.099   9.222
summary.peRes           8.957  0.118   9.093
peEdgeRenderInfo        8.640  0.122   8.778
pe                      8.466  0.122   8.599
pDis                    8.034  0.218   8.267
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ROntoTools.Rcheck/00check.log’
for details.



Installation output

ROntoTools.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.max, which.min


Attaching package: 'KEGGgraph'

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

    plot

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

    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 5.970713 secs.


RUNIT TEST PROTOCOL -- Tue Jun 15 23:15:29 2021 
*********************************************** 
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 
 17.719   0.541  18.255 

Example timings

ROntoTools.Rcheck/ROntoTools-Ex.timings

nameusersystemelapsed
alpha1MR0.0560.0030.060
alphaMLG0.0190.0010.020
compute.fisher0.0000.0010.001
compute.normalInv0.0010.0000.001
keggPathwayGraphs0.7260.0140.742
keggPathwayNames0.4110.0090.419
nodeWeights0.0060.0010.007
pDis8.0340.2188.267
pe8.4660.1228.599
peEdgeRenderInfo8.6400.1228.778
peNodeRenderInfo 9.889 0.13210.035
plot.pePathway-methods9.3410.1309.539
plot.peRes-methods12.696 0.11212.823
setEdgeWeights2.9290.0322.971
setNodeWeights0.6800.0040.685
summary.pDisRes9.0970.0999.222
summary.peRes8.9570.1189.093