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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 89/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
apComplex 2.72.0  (landing page)
Denise Scholtens
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/apComplex
git_branch: RELEASE_3_20
git_last_commit: 9bf087b
git_last_commit_date: 2024-10-29 09:23:59 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for apComplex on kjohnson1

To the developers/maintainers of the apComplex package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: apComplex
Version: 2.72.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:apComplex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings apComplex_2.72.0.tar.gz
StartedAt: 2024-12-20 11:19:50 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 11:21:54 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 123.8 seconds
RetCode: 0
Status:   OK  
CheckDir: apComplex.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:apComplex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings apComplex_2.72.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/apComplex.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘apComplex/DESCRIPTION’ ... OK
* this is package ‘apComplex’ version ‘2.72.0’
* 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 code 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 ... 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-3.20-bioc/meat/apComplex.Rcheck/00check.log’
for details.


Installation output

apComplex.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL apComplex
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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
FilteredEstimates0.0470.0040.052
HMSPCI0.0540.0070.061
Krogan0.0050.0020.007
LCjoin0.7390.0090.748
MBMEcHMSPCI0.0060.0020.008
MBMEcKrogan0.0010.0020.004
MBMEcTAP0.0090.0020.011
TAP0.0330.0040.038
apEX0.0020.0030.005
bhmaxSubgraph0.0460.0050.051
findComplexes0.0230.0040.027
gavinBP20060.1570.0220.180
kroganBPMat20060.4250.0480.473
mergeComplexes0.0250.0100.035
plotComplex0.0830.0070.090
sortComplexes0.0250.0040.028
yNameTAP0.0160.0100.025
yTAP0.0040.0050.010