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CHECK report for apComplex on merida1

This page was generated on 2020-08-10 12:29:59 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE apComplex PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 71/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
apComplex 2.55.0
Denise Scholtens
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/apComplex
Branch: master
Last Commit: f952b2e
Last Changed Date: 2020-04-27 14:10:49 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: apComplex
Version: 2.55.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:apComplex.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings apComplex_2.55.0.tar.gz
StartedAt: 2020-08-09 22:41:25 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 22:43:24 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 118.5 seconds
RetCode: 0
Status:  OK 
CheckDir: apComplex.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:apComplex.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings apComplex_2.55.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/apComplex.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘apComplex/DESCRIPTION’ ... OK
* this is package ‘apComplex’ version ‘2.55.0’
* 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 ‘apComplex’ 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘RBGL’ ‘graph’
  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
plotComplex: warning in mget(complexMembers, env = org.Sc.sgdGENENAME,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
bhmaxSubgraph: no visible global function definition for ‘as’
bhmaxSubgraph: no visible global function definition for ‘ugraph’
bhmaxSubgraph: no visible global function definition for ‘maxClique’
plotComplex: no visible global function definition for ‘subGraph’
plotComplex: no visible global function definition for
  ‘removeSelfLoops’
plotComplex: no visible global function definition for ‘edgeNames’
plotComplex: no visible global function definition for ‘numEdges’
plotComplex: no visible global function definition for ‘degree’
Undefined global functions or variables:
  as degree edgeNames maxClique numEdges removeSelfLoops subGraph
  ugraph
Consider adding
  importFrom("methods", "as")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/apComplex.Rcheck/00check.log’
for details.



Installation output

apComplex.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL apComplex
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘apComplex’ ...
** using staged installation
** R
** data
** 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 (apComplex)

Tests output


Example timings

apComplex.Rcheck/apComplex-Ex.timings

nameusersystemelapsed
FilteredEstimates0.0530.0070.061
HMSPCI0.0590.0090.068
Krogan0.0070.0010.008
LCjoin0.4300.0110.442
MBMEcHMSPCI0.0080.0020.009
MBMEcKrogan0.0020.0020.004
MBMEcTAP0.0090.0020.010
TAP0.0430.0060.048
apEX0.0020.0020.005
bhmaxSubgraph0.0720.0100.082
findComplexes0.0320.0050.037
gavinBP20060.2060.0270.235
kroganBPMat20060.5650.0630.629
mergeComplexes0.0230.0120.035
plotComplex0.1170.0070.123
sortComplexes0.0270.0060.034
yNameTAP0.0200.0110.032
yTAP0.0040.0070.012