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CHECK report for apComplex on malbec1

This page was generated on 2020-08-07 11:15:15 -0400 (Fri, 07 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: 2020-08-06 14:50:46 -0400 (Thu, 06 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
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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:apComplex.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings apComplex_2.55.0.tar.gz
StartedAt: 2020-08-06 22:36:33 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 22:38:12 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 99.0 seconds
RetCode: 0
Status:  OK 
CheckDir: apComplex.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:apComplex.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings apComplex_2.55.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/apComplex.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/apComplex.Rcheck/00check.log’
for details.



Installation output

apComplex.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL apComplex
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
FilteredEstimates0.0880.0040.090
HMSPCI0.0680.0040.074
Krogan0.0040.0000.004
LCjoin0.4320.0040.439
MBMEcHMSPCI0.0080.0000.004
MBMEcKrogan0.0000.0000.002
MBMEcTAP0.0080.0000.007
TAP0.0200.0080.026
apEX0.0000.0000.003
bhmaxSubgraph0.0520.0000.052
findComplexes0.0200.0000.021
gavinBP20060.0760.0360.110
kroganBPMat20060.2280.0640.295
mergeComplexes0.0200.0080.029
plotComplex0.0880.0000.088
sortComplexes0.0200.0040.024
yNameTAP0.0120.0000.011
yTAP0.0040.0000.004