Multiple platform build/check report for BioC 3.6 - CHECK report for ScISI on tokay1

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### Running command:
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###   rm -rf ScISI.buildbin-libdir ScISI.Rcheck && mkdir ScISI.buildbin-libdir ScISI.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ScISI.buildbin-libdir ScISI_1.50.0.tar.gz >ScISI.Rcheck\00install.out 2>&1 && cp ScISI.Rcheck\00install.out ScISI-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ScISI.buildbin-libdir --install="check:ScISI-install.out" --force-multiarch --no-vignettes --timings ScISI_1.50.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ScISI.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.50.0'
* 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-3.6-bioc/meat/ScISI.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ScISI' ...
** R
** data
** inst
** preparing 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
  converting help for package 'ScISI'
    finding HTML links ... done
    Desc-methods                            html  
    ID-methods                              html  
    JaccardCoef                             html  
    ScISI                                   html  
    ScISI2html                              html  
    arp23                                   html  
    arp23G                                  html  
    arp23Orf                                html  
    arp23Y2HG                               html  
    calcGraphStats                          html  
    cfia                                    html  
    cfiaOrf                                 html  
    checkComplex                            html  
    checkSGN                                html  
    compBijection                           html  
    compareComplex                          html  
    createGODataFrame                       html  
    createGOMatrix                          html  
    createMipsDataFrame                     html  
    createMipsMatrix                        html  
    createYeastDataObj                      html  
    dataS                                   html  
    eAt                                     html  
    eAt2                                    html  
    edgeProp                                html  
    egEBI16112                              html  
    expStats                                html  
    findSubComp                             html  
    gavin2mergeMG                           html  
    getAPMSData                             html  
    getGOInfo                               html  
    getLocOrfs                              html  
    getMipsInfo                             html  
    getURL-methods                          html  
    graphSumStats                           html  
    ho2mergeMGG                             html  
    krogan2mergeMGGH                        html  
    locScISI                                html  
    mapping2SysG                            html  
    mappingsG                               html  
    maximizeSimilarity                      html  
    meanDeg                                 html  
    mergeBGMat                              html  
    mips2go                                 html  
    nAt                                     html  
    nAtMap                                  html  
    nonGenes                                html  
    nucComp                                 html  
    recCompSize                             html  
    redundantM                              html  
    rmByEvi                                 html  
    runAlignment                            html  
    runCompareComplex                       html  
    subCompM                                html  
    sumStats                                html  
    unWantedComp                            html  
    unwanted                                html  
    xtraGO                                  html  
    xtraGONodes                             html  
    yeastData-class                         html  
** 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'
In R CMD INSTALL

install for x64

* installing *source* package 'ScISI' ...
** 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'
* MD5 sums
packaged installation of 'ScISI' as ScISI_1.50.0.zip
* DONE (ScISI)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for ScISI on tokay1

Summary

Command output

Installation output

Tests output

Example timings