Package: PCAN

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PCAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PCAN_1.10.0.tar.gz

StartedAt: 2019-04-13 04:26:02 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:33:30 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 448.0 seconds

RetCode: 0

Status:  OK

CheckDir: PCAN.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PCAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PCAN_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/PCAN.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PCAN/DESCRIPTION' ... OK
* this is package 'PCAN' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'PCAN' 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 ... OK
* 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 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
Examples with CPU or elapsed time > 5s
                    user system elapsed
hpGeneListComp     62.67   1.89   64.72
hpGeneHeatmap      43.58   1.30   44.91
compareHPSets      39.86   0.13   39.99
hpSetCompBestMatch  5.10   0.03    5.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
hpGeneHeatmap  47.86   0.14   48.00
hpGeneListComp 47.43   0.13   47.61
compareHPSets  46.21   0.17   46.37
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/PCAN_1.10.0.tar.gz && rm -rf PCAN.buildbin-libdir && mkdir PCAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PCAN.buildbin-libdir PCAN_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL PCAN_1.10.0.zip && rm PCAN_1.10.0.tar.gz PCAN_1.10.0.zip
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install for i386

* installing *source* package 'PCAN' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PCAN'
    finding HTML links ... done
    calcHpSim                               html  
    compareHPSets                           html  
    finding level-2 HTML links ... done

    computeHpIC                             html  
    geneByHp                                html  
    geneByTrait                             html  
    geneDef                                 html  
    hpByTrait                               html  
    hpDef                                   html  
    hpGeneHeatmap                           html  
    hpGeneListComp                          html  
    hpSetCompBestMatch                      html  
    hpSetCompSummary                        html  
    hp_ancestors                            html  
    hp_class                                html  
    hp_descendants                          html  
    hqStrNw                                 html  
    hsEntrezByRPath                         html  
    rPath                                   html  
    traitDef                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PCAN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PCAN' as PCAN_1.10.0.zip
* DONE (PCAN)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'PCAN' successfully unpacked and MD5 sums checked
In R CMD INSTALL