Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:04 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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 70/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
apComplex 2.63.0  (landing page)
Denise Scholtens
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/apComplex
git_branch: master
git_last_commit: a54a96e
git_last_commit_date: 2022-04-26 10:56:39 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: apComplex
Version: 2.63.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:apComplex.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings apComplex_2.63.0.tar.gz
StartedAt: 2022-06-23 23:11:59 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:13:53 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 114.1 seconds
RetCode: 0
Status:   OK  
CheckDir: apComplex.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:apComplex.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings apComplex_2.63.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/apComplex.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'apComplex/DESCRIPTION' ... OK
* this is package 'apComplex' version '2.63.0'
* 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 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
  'F:/biocbuild/bbs-3.16-bioc/meat/apComplex.Rcheck/00check.log'
for details.



Installation output

apComplex.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/apComplex_2.63.0.tar.gz && rm -rf apComplex.buildbin-libdir && mkdir apComplex.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=apComplex.buildbin-libdir apComplex_2.63.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL apComplex_2.63.0.zip && rm apComplex_2.63.0.tar.gz apComplex_2.63.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  472k  100  472k    0     0  4928k      0 --:--:-- --:--:-- --:--:-- 4974k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'apComplex' as apComplex_2.63.0.zip
* DONE (apComplex)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'apComplex' successfully unpacked and MD5 sums checked

Tests output


Example timings

apComplex.Rcheck/apComplex-Ex.timings

nameusersystemelapsed
FilteredEstimates0.050.000.04
HMSPCI0.030.010.05
Krogan000
LCjoin0.580.000.58
MBMEcHMSPCI000
MBMEcKrogan0.000.020.01
MBMEcTAP000
TAP0.000.030.03
apEX0.020.000.02
bhmaxSubgraph0.040.000.04
findComplexes0.030.000.04
gavinBP20060.080.000.07
kroganBPMat20060.210.020.22
mergeComplexes0.030.000.03
plotComplex0.090.000.10
sortComplexes0.030.000.03
yNameTAP000
yTAP0.000.010.01