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CHECK report for ScISI on malbec1

This page was generated on 2019-04-16 11:48:09 -0400 (Tue, 16 Apr 2019).

Package 1397/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ScISI 1.54.0
Tony Chiang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ScISI
Branch: RELEASE_3_8
Last Commit: c9a6a97
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ScISI
Version: 1.54.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ScISI_1.54.0.tar.gz
StartedAt: 2019-04-16 02:54:09 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:55:45 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 96.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ScISI.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ScISI_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ScISI.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ScISI/DESCRIPTION’ ... OK
* this is package ‘ScISI’ version ‘1.54.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
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.
* 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’
Undefined global functions or variables:
  MBMEcHMSPCI MBMEcKrogan ScISI nonGenes unwanted xtraGO yNameTAP
* 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 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/ScISI.Rcheck/00check.log’
for details.



Installation output

ScISI.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ScISI
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘ScISI’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
* DONE (ScISI)

Tests output


Example timings

ScISI.Rcheck/ScISI-Ex.timings

nameusersystemelapsed
JaccardCoef000
ScISI0.0280.0080.037
ScISI2html000
arp230.0040.0000.002
arp23G0.0000.0000.002
arp23Orf0.0040.0000.002
arp23Y2HG0.0000.0000.002
cfia0.0040.0000.003
cfiaOrf0.0000.0000.002
createGODataFrame000
createGOMatrix000
createMipsMatrix000
createYeastDataObj0.0000.0000.001
dataS0.0000.0000.001
eAt0.0000.0000.002
eAt20.0040.0000.002
egEBI161120.0000.0000.001
expStats0.0240.0040.027
findSubComp0.0040.0000.001
gavin2mergeMG0.0080.0000.010
getAPMSData0.2400.1720.493
getGOInfo000
getMipsInfo000
ho2mergeMGG0.0080.0000.007
krogan2mergeMGGH0.0080.0000.005
locScISI0.0800.0240.105
mapping2SysG0.0000.0000.003
mappingsG0.0040.0000.002
maximizeSimilarity0.0000.0000.001
mergeBGMat000
mips2go0.0000.0040.006
nAtMap0.0000.0000.002
nonGenes0.0000.0000.003
nucComp0.0040.0000.002
recCompSize000
redundantM0.0000.0000.002
runAlignment000
runCompareComplex0.0000.0000.001
subCompM0.0040.0000.002
sumStats000
unWantedComp000
unwanted0.0000.0000.003
xtraGO0.0040.0000.002
yeastData-class0.0000.0000.001