BioC 3.1: CHECK report for apComplex on petty
This page was generated on 2015-10-09 09:32:45 -0700 (Fri, 09 Oct 2015).
apComplex 2.34.0 Denise Scholtens
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/apComplex | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
Package: apComplex |
Version: 2.34.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings apComplex_2.34.0.tar.gz |
StartedAt: 2015-10-08 21:28:38 -0700 (Thu, 08 Oct 2015) |
EndedAt: 2015-10-08 21:30:53 -0700 (Thu, 08 Oct 2015) |
EllapsedTime: 135.0 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 --no-vignettes --timings apComplex_2.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/apComplex.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘apComplex/DESCRIPTION’ ... OK
* this is package ‘apComplex’ version ‘2.34.0’
* 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 ... [14s/14s] 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:
‘graph’ ‘RBGL’
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 ‘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’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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-3.1-bioc/meat/apComplex.Rcheck/00check.log’
for details.
apComplex.Rcheck/00install.out:
* installing *source* package ‘apComplex’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (apComplex)
apComplex.Rcheck/apComplex-Ex.timings:
name | user | system | elapsed
|
FilteredEstimates | 0.076 | 0.009 | 0.086 |
|
HMSPCI | 0.077 | 0.020 | 0.099 |
|
Krogan | 0.179 | 0.001 | 0.180 |
|
LCjoin | 0.320 | 0.011 | 0.356 |
|
MBMEcHMSPCI | 0.009 | 0.002 | 0.011 |
|
MBMEcKrogan | 0.004 | 0.001 | 0.005 |
|
MBMEcTAP | 0.015 | 0.002 | 0.017 |
|
TAP | 0.041 | 0.016 | 0.057 |
|
apEX | 0.006 | 0.001 | 0.007 |
|
bhmaxSubgraph | 0.222 | 0.008 | 0.231 |
|
findComplexes | 0.031 | 0.008 | 0.039 |
|
gavinBP2006 | 0.178 | 0.063 | 0.241 |
|
kroganBPMat2006 | 0.473 | 0.151 | 0.625 |
|
mergeComplexes | 0.030 | 0.032 | 0.062 |
|
plotComplex | 0.080 | 0.011 | 0.120 |
|
sortComplexes | 0.030 | 0.009 | 0.039 |
|
yNameTAP | 0.020 | 0.049 | 0.069 |
|
yTAP | 0.009 | 0.048 | 0.057 |
|