BioC 3.1: CHECK report for apComplex on zin2

Package: apComplex

Version: 2.34.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings apComplex_2.34.0.tar.gz

StartedAt: 2015-10-08 22:31:24 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:32:34 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 70.3 seconds

RetCode: 0

Status:  OK

CheckDir: apComplex.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings apComplex_2.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/apComplex.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.34.0’
* 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 ... [8s/8s] 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 ‘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 ... [4s/4s] 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-3.1-bioc/meat/apComplex.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
FilteredEstimates	0.042	0.000	0.042
HMSPCI	0.047	0.004	0.052
Krogan	0.122	0.004	0.125
LCjoin	0.188	0.004	0.192
MBMEcHMSPCI	0.005	0.000	0.005
MBMEcKrogan	0.002	0.000	0.002
MBMEcTAP	0.008	0.000	0.008
TAP	0.025	0.000	0.025
apEX	0.003	0.000	0.003
bhmaxSubgraph	0.139	0.000	0.139
findComplexes	0.017	0.004	0.021
gavinBP2006	0.096	0.004	0.100
kroganBPMat2006	0.253	0.008	0.261
mergeComplexes	0.021	0.000	0.021
plotComplex	0.033	0.008	0.044
sortComplexes	0.012	0.008	0.020
yNameTAP	0.007	0.004	0.011
yTAP	0.005	0.000	0.005