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CHECK report for ScISI on malbec2

This page was generated on 2020-10-17 11:55:41 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ScISI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1597/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ScISI 1.60.0
Tony Chiang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ScISI
Branch: RELEASE_3_11
Last Commit: 8057b08
Last Changed Date: 2020-04-27 14:12:48 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ScISI
Version: 1.60.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ScISI_1.60.0.tar.gz
StartedAt: 2020-10-17 05:13:33 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:15:40 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 126.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ScISI.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ScISI.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ScISI_1.60.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ScISI.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.60.0’
* 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-3.11-bioc/meat/ScISI.Rcheck/00check.log’
for details.



Installation output

ScISI.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ScISI
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘ScISI’ ...
** using staged installation
** 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 from temporary location
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’
** testing if installed package can be loaded from final location
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’
** testing if installed package keeps a record of temporary installation path
* DONE (ScISI)

Tests output


Example timings

ScISI.Rcheck/ScISI-Ex.timings

nameusersystemelapsed
JaccardCoef000
ScISI0.0310.0040.034
ScISI2html0.0000.0000.001
arp230.0020.0000.002
arp23G0.0020.0000.001
arp23Orf0.0010.0000.002
arp23Y2HG0.0010.0000.002
cfia0.0010.0000.002
cfiaOrf0.0010.0000.001
createGODataFrame000
createGOMatrix0.0000.0000.001
createMipsMatrix000
createYeastDataObj0.0010.0000.000
dataS0.0010.0000.002
eAt0.0010.0000.002
eAt20.0010.0000.001
egEBI161120.0010.0000.001
expStats0.0020.0000.001
findSubComp000
gavin2mergeMG0.0050.0000.006
getAPMSData0.2150.1560.379
getGOInfo0.0000.0000.001
getMipsInfo000
ho2mergeMGG0.0080.0040.012
krogan2mergeMGGH0.0070.0000.006
locScISI0.0950.0160.138
mapping2SysG0.0000.0020.003
mappingsG0.0020.0010.014
maximizeSimilarity000
mergeBGMat000
mips2go0.0070.0000.016
nAtMap0.0000.0020.002
nonGenes0.0020.0010.002
nucComp0.0030.0000.003
recCompSize000
redundantM0.0020.0000.002
runAlignment0.0000.0000.001
runCompareComplex0.0010.0000.000
subCompM0.0010.0000.001
sumStats000
unWantedComp000
unwanted0.0010.0000.001
xtraGO0.0010.0000.001
yeastData-class000