BioC 2.14: CHECK report for ScISI on petty

Package: ScISI

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ScISI_1.36.0.tar.gz

StartedAt: 2014-10-08 00:04:57 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:09:34 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 276.5 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ScISI_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ScISI.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ScISI/DESCRIPTION’ ... OK
* this is package ‘ScISI’ version ‘1.36.0’
* 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 ‘ScISI’ can be installed ... [24s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GO.db’ ‘RpsiXML’ ‘annotate’
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: ‘apComplex’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGOInfo : <anonymous>: warning in
  mget(names(parsed[[z]])[these[[z]]], env = org.Sc.sgdGO2ORF,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
getGOInfo: warning in mget(names(cMembers), env = GOCCCHILDREN,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
getGOInfo: warning in mget(names(comp)[alsoThese], env =
  org.Sc.sgdGO2ORF, ifnotfound = NA): partial argument match of 'env'
  to 'envir'
checkComplex: no visible binding for global variable ‘ScISI’
getAPMSData: no visible binding for global variable ‘yNameTAP’
getAPMSData: no visible binding for global variable ‘MBMEcHMSPCI’
getAPMSData: no visible binding for global variable ‘MBMEcKrogan’
getGOInfo: no visible binding for global variable ‘xtraGO’
getGOInfo: no visible binding for global variable ‘unwanted’
getMipsInfo: no visible binding for global variable ‘nonGenes’
* checking Rd files ... NOTE
prepare_Rd: arp23Orf.Rd:14-15: Dropping empty section \details
prepare_Rd: calcGraphStats.Rd:63: Dropping empty section \references
prepare_Rd: calcGraphStats.Rd:66-70: Dropping empty section \examples
prepare_Rd: checkComplex.Rd:47-48: Dropping empty section \examples
prepare_Rd: checkSGN.Rd:24-25: Dropping empty section \note
prepare_Rd: checkSGN.Rd:26-28: Dropping empty section \examples
prepare_Rd: compBijection.Rd:68-69: Dropping empty section \examples
prepare_Rd: compareComplex.Rd:45-47: Dropping empty section \examples
prepare_Rd: createMipsDataFrame.Rd:35-37: Dropping empty section \examples
prepare_Rd: edgeProp.Rd:25-27: Dropping empty section \details
prepare_Rd: edgeProp.Rd:37-39: Dropping empty section \examples
prepare_Rd: getLocOrfs.Rd:60-61: Dropping empty section \examples
prepare_Rd: graphSumStats.Rd:20-22: Dropping empty section \details
prepare_Rd: graphSumStats.Rd:47-49: Dropping empty section \examples
prepare_Rd: meanDeg.Rd:21-23: Dropping empty section \details
prepare_Rd: meanDeg.Rd:28-29: Dropping empty section \examples
prepare_Rd: rmByEvi.Rd:40-42: Dropping empty section \examples
prepare_Rd: runCompareComplex.Rd:23-25: Dropping empty section \details
prepare_Rd: subCompM.Rd:16-18: Dropping empty section \details
prepare_Rd: sumStats.Rd:24-26: Dropping empty section \details
prepare_Rd: xtraGONodes.Rd:25-27: Dropping empty section \examples
* 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 ... [14s/16s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/ScISI.Rcheck/00check.log’
for details.

* installing *source* package ‘ScISI’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ScISI)

name	user	system	elapsed
JaccardCoef	0.001	0.000	0.002
ScISI	0.291	0.018	0.311
ScISI2html	0.002	0.000	0.002
arp23	0.004	0.001	0.005
arp23G	0.004	0.000	0.005
arp23Orf	0.004	0.001	0.005
arp23Y2HG	0.003	0.001	0.004
cfia	0.003	0.001	0.004
cfiaOrf	0.004	0.001	0.004
createGODataFrame	0.001	0.000	0.001
createGOMatrix	0.001	0.000	0.001
createMipsMatrix	0.001	0.001	0.001
createYeastDataObj	0.001	0.000	0.002
dataS	0.003	0.000	0.004
eAt	0.004	0.001	0.005
eAt2	0.004	0.001	0.004
egEBI16112	0.004	0.001	0.004
expStats	0.003	0.001	0.004
findSubComp	0.001	0.000	0.001
gavin2mergeMG	0.013	0.008	0.021
getAPMSData	0.522	0.491	2.465
getGOInfo	0.002	0.001	0.002
getMipsInfo	0.001	0.000	0.001
ho2mergeMGG	0.019	0.008	0.027
krogan2mergeMGGH	0.010	0.008	0.018
locScISI	1.050	0.049	1.127
mapping2SysG	0.004	0.001	0.013
mappingsG	0.004	0.001	0.004
maximizeSimilarity	0.002	0.000	0.001
mergeBGMat	0.001	0.000	0.002
mips2go	0.008	0.001	0.010
nAtMap	0.004	0.001	0.004
nonGenes	0.003	0.001	0.005
nucComp	0.004	0.000	0.007
recCompSize	0.001	0.000	0.002
redundantM	0.003	0.001	0.004
runAlignment	0.001	0.000	0.001
runCompareComplex	0.001	0.000	0.002
subCompM	0.004	0.001	0.004
sumStats	0.002	0.000	0.003
unWantedComp	0.001	0.000	0.001
unwanted	0.003	0.001	0.004
xtraGO	0.003	0.001	0.004
yeastData-class	0.001	0.000	0.001