Package: apComplex

Version: 2.49.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:apComplex.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings apComplex_2.49.1.tar.gz

StartedAt: 2019-04-09 01:06:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:08:39 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 129.3 seconds

RetCode: 0

Status:  OK

CheckDir: apComplex.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:apComplex.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings apComplex_2.49.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/apComplex.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'apComplex/DESCRIPTION' ... OK
* this is package 'apComplex' version '2.49.1'
* 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 'apComplex' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  'RBGL' 'graph'
  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
plotComplex: warning in mget(complexMembers, env = org.Sc.sgdGENENAME,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
bhmaxSubgraph: no visible global function definition for 'as'
bhmaxSubgraph: no visible global function definition for 'ugraph'
bhmaxSubgraph: no visible global function definition for 'maxClique'
plotComplex: no visible global function definition for 'subGraph'
plotComplex: no visible global function definition for
  'removeSelfLoops'
plotComplex: no visible global function definition for 'edgeNames'
plotComplex: no visible global function definition for 'numEdges'
plotComplex: no visible global function definition for 'degree'
Undefined global functions or variables:
  as degree edgeNames maxClique numEdges removeSelfLoops subGraph
  ugraph
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 ...
** 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/apComplex.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/apComplex_2.49.1.tar.gz && rm -rf apComplex.buildbin-libdir && mkdir apComplex.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=apComplex.buildbin-libdir apComplex_2.49.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL apComplex_2.49.1.zip && rm apComplex_2.49.1.tar.gz apComplex_2.49.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  471k  100  471k    0     0  8037k      0 --:--:-- --:--:-- --:--:-- 9068k

install for i386

* installing *source* package 'apComplex' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'apComplex'
    finding HTML links ... done
    FilteredEstimates                       html  
    HMSPCI                                  html  
    Krogan                                  html  
    LCjoin                                  html  
    MBMEcHMSPCI                             html  
    MBMEcKrogan                             html  
    MBMEcTAP                                html  
    TAP                                     html  
    apEX                                    html  
    bhmaxSubgraph                           html  
    findComplexes                           html  
    gavinBP2006                             html  
    kroganBPMat2006                         html  
    mergeComplexes                          html  
    plotComplex                             html  
    sortComplexes                           html  
    yNameTAP                                html  
    yTAP                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'apComplex' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'apComplex' as apComplex_2.49.1.zip
* DONE (apComplex)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'apComplex' successfully unpacked and MD5 sums checked