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BioC 3.5: CHECK report for ScISI on tokay2

This page was generated on 2017-08-16 13:19:09 -0400 (Wed, 16 Aug 2017).

Package 1189/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ScISI 1.48.0
Tony Chiang
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ScISI
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ScISI
Version: 1.48.0
Command: rm -rf ScISI.buildbin-libdir ScISI.Rcheck && mkdir ScISI.buildbin-libdir ScISI.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ScISI.buildbin-libdir ScISI_1.48.0.tar.gz >ScISI.Rcheck\00install.out 2>&1 && cp ScISI.Rcheck\00install.out ScISI-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ScISI.buildbin-libdir --install="check:ScISI-install.out" --force-multiarch --no-vignettes --timings ScISI_1.48.0.tar.gz
StartedAt: 2017-08-16 02:46:21 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:49:00 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 158.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ScISI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ScISI.buildbin-libdir ScISI.Rcheck && mkdir ScISI.buildbin-libdir ScISI.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ScISI.buildbin-libdir ScISI_1.48.0.tar.gz >ScISI.Rcheck\00install.out 2>&1 && cp ScISI.Rcheck\00install.out ScISI-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ScISI.buildbin-libdir --install="check:ScISI-install.out" --force-multiarch --no-vignettes --timings ScISI_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ScISI.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ScISI/DESCRIPTION' ... OK
* this is package 'ScISI' version '1.48.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ScISI.Rcheck/00check.log'
for details.


ScISI.Rcheck/00install.out:


install for i386

* installing *source* package 'ScISI' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst

install for x64

* installing *source* package 'ScISI' ...
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* MD5 sums
packaged installation of 'ScISI' as ScISI_1.48.0.zip
* DONE (ScISI)

ScISI.Rcheck/examples_i386/ScISI-Ex.timings:

nameusersystemelapsed
JaccardCoef000
ScISI0.040.010.06
ScISI2html000
arp230.000.020.02
arp23G000
arp23Orf0.000.010.02
arp23Y2HG000
cfia0.000.020.01
cfiaOrf000
createGODataFrame000
createGOMatrix000
createMipsMatrix000
createYeastDataObj000
dataS000
eAt0.000.010.01
eAt2000
egEBI161120.000.020.02
expStats000
findSubComp000
gavin2mergeMG0.000.010.01
getAPMSData0.220.190.43
getGOInfo000
getMipsInfo000
ho2mergeMGG0.010.000.01
krogan2mergeMGGH0.020.000.02
locScISI0.410.020.42
mapping2SysG0.000.010.01
mappingsG0.010.000.02
maximizeSimilarity000
mergeBGMat000
mips2go0.020.000.02
nAtMap0.010.000.01
nonGenes0.000.020.02
nucComp0.000.010.01
recCompSize000
redundantM000
runAlignment000
runCompareComplex000
subCompM0.020.000.02
sumStats000
unWantedComp000
unwanted000
xtraGO0.000.020.02
yeastData-class000

ScISI.Rcheck/examples_x64/ScISI-Ex.timings:

nameusersystemelapsed
JaccardCoef000
ScISI0.030.020.05
ScISI2html000
arp230.000.010.02
arp23G000
arp23Orf000
arp23Y2HG0.010.000.02
cfia000
cfiaOrf0.000.010.02
createGODataFrame000
createGOMatrix000
createMipsMatrix000
createYeastDataObj000
dataS0.020.000.01
eAt000
eAt2000
egEBI161120.000.020.01
expStats0.000.020.02
findSubComp000
gavin2mergeMG0.020.010.03
getAPMSData0.230.170.44
getGOInfo000
getMipsInfo000
ho2mergeMGG0.240.000.23
krogan2mergeMGGH0.000.020.02
locScISI0.370.000.37
mapping2SysG0.020.000.02
mappingsG000
maximizeSimilarity000
mergeBGMat000
mips2go000
nAtMap000
nonGenes0.020.000.01
nucComp0.000.010.02
recCompSize000
redundantM0.000.020.02
runAlignment000
runCompareComplex000
subCompM0.020.000.02
sumStats000
unWantedComp000
unwanted0.000.020.01
xtraGO0.020.000.01
yeastData-class000