Package: ppiStats

Version: 1.50.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ppiStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ppiStats_1.50.0.tar.gz

StartedAt: 2019-10-16 06:05:54 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:09:37 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 222.6 seconds

RetCode: 0

Status:  OK

CheckDir: ppiStats.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ppiStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ppiStats_1.50.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ppiStats.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ppiStats/DESCRIPTION' ... OK
* this is package 'ppiStats' 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 'ppiStats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice'
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
Packages in Depends field not imported from:
  'ScISI' 'ppiData'
  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 ... OK
* checking Rd files ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
estimatePPIErrorRates 4.14   0.42    6.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
estimatePPIErrorRates  4.4   0.67    5.06
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ppiStats.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ppiStats_1.50.0.tar.gz && rm -rf ppiStats.buildbin-libdir && mkdir ppiStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ppiStats.buildbin-libdir ppiStats_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ppiStats_1.50.0.zip && rm ppiStats_1.50.0.tar.gz ppiStats_1.50.0.zip
###
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100 1017k  100 1017k    0     0  15.5M      0 --:--:-- --:--:-- --:--:-- 17.1M

install for i386

* installing *source* package 'ppiStats' ...
** using staged installation
** R
** 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
  converting help for package 'ppiStats'
    finding HTML links ... done
    assessSymmetry                          html  
    bpMatrix                                html  
    calcInOutDegStats                       html  
    createSummaryTables                     html  
    degreeEstimates                         html  
    estErrProbMethodOfMoments               html  
    estimateCCMErrorRates                   html  
    estimatePPIErrorRates                   html  
    findAdjacent                            html  
    genBPGraph                              html  
    hgParams                                html  
    hgTests                                 html  
    idProteinErrorType                      html  
    idProteinType                           html  
    inOutScatterCharts                      html  
    nullDistDoublyTestedEdges               html  
    separateExptBySize                      html  
    twPERM                                  html  
    viabilityCharts                         html  
** 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

install for x64

* installing *source* package 'ppiStats' ...
** 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 'ppiStats' as ppiStats_1.50.0.zip
* DONE (ppiStats)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ppiStats' successfully unpacked and MD5 sums checked