BioC 2.13: CHECK report for ScISI on zin1

Package: ScISI

Version: 1.34.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ScISI_1.34.0.tar.gz

StartedAt: 2014-04-05 03:51:57 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:53:52 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 115.1 seconds

RetCode: 0

Status:  OK

CheckDir: ScISI.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ScISI.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ScISI/DESCRIPTION’ ... OK
* this is package ‘ScISI’ version ‘1.34.0’
* 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 ‘ScISI’ can be installed ... [12s/12s] 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [7s/7s] 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 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.004	0.000	0.003
ScISI	0.164	0.000	0.163
ScISI2html	0.004	0.000	0.004
arp23	0.004	0.000	0.004
arp23G	0.004	0.000	0.003
arp23Orf	0.004	0.000	0.003
arp23Y2HG	0.004	0.000	0.003
cfia	0.004	0.000	0.003
cfiaOrf	0.004	0.000	0.005
createGODataFrame	0.004	0.000	0.002
createGOMatrix	0.004	0.000	0.002
createMipsMatrix	0.000	0.000	0.002
createYeastDataObj	0.000	0.000	0.002
dataS	0.004	0.000	0.004
eAt	0.004	0.000	0.004
eAt2	0.004	0.000	0.004
egEBI16112	0.004	0.000	0.004
expStats	0.004	0.000	0.006
findSubComp	0.004	0.000	0.002
gavin2mergeMG	0.004	0.004	0.010
getAPMSData	0.344	0.140	0.488
getGOInfo	0.004	0.000	0.005
getMipsInfo	0.004	0.000	0.002
ho2mergeMGG	0.012	0.000	0.010
krogan2mergeMGGH	0.008	0.000	0.009
locScISI	0.480	0.016	0.497
mapping2SysG	0.004	0.000	0.002
mappingsG	0.004	0.000	0.004
maximizeSimilarity	0.000	0.004	0.004
mergeBGMat	0.000	0.000	0.001
mips2go	0.004	0.000	0.005
nAtMap	0.004	0.000	0.002
nonGenes	0.004	0.000	0.004
nucComp	0.004	0.000	0.003
recCompSize	0.000	0.000	0.001
redundantM	0.004	0.000	0.002
runAlignment	0.004	0.000	0.002
runCompareComplex	0.004	0.000	0.004
subCompM	0.000	0.000	0.002
sumStats	0.000	0.000	0.001
unWantedComp	0.004	0.000	0.001
unwanted	0.000	0.000	0.002
xtraGO	0.000	0.000	0.003
yeastData-class	0.004	0.000	0.003