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This page was generated on 2023-04-12 11:04:58 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for apComplex on nebbiolo2


To the developers/maintainers of the apComplex package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/apComplex.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 70/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
apComplex 2.64.0  (landing page)
Denise Scholtens
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/apComplex
git_branch: RELEASE_3_16
git_last_commit: d2667d0
git_last_commit_date: 2022-11-01 10:38:32 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: apComplex
Version: 2.64.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:apComplex.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings apComplex_2.64.0.tar.gz
StartedAt: 2023-04-10 19:00:02 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:01:55 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 112.3 seconds
RetCode: 0
Status:   OK  
CheckDir: apComplex.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:apComplex.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings apComplex_2.64.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/apComplex.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘apComplex/DESCRIPTION’ ... OK
* this is package ‘apComplex’ version ‘2.64.0’
* 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 loading without being on the library search path ... 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 ...
  ‘apComplex.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/apComplex.Rcheck/00check.log’
for details.



Installation output

apComplex.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL apComplex
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
FilteredEstimates0.0370.0000.037
HMSPCI0.0430.0000.043
Krogan0.0040.0000.004
LCjoin0.7560.0040.759
MBMEcHMSPCI0.0040.0000.004
MBMEcKrogan0.0010.0000.001
MBMEcTAP0.0070.0000.006
TAP0.0260.0000.026
apEX0.0010.0010.002
bhmaxSubgraph0.0410.0030.043
findComplexes0.0200.0030.024
gavinBP20060.0770.0370.113
kroganBPMat20060.2160.0840.301
mergeComplexes0.0190.0080.027
plotComplex0.0730.0000.073
sortComplexes0.0240.0000.023
yNameTAP0.0110.0000.011
yTAP0.0000.0030.004