Multiple platform build/check report for BioC 3.9 - CHECK report for PANR on tokay2

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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:PANR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PANR_1.29.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PANR.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 'PANR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PANR' version '1.29.1'
* 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 'PANR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:21: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:85: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:85: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:89: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:89: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:9: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:44: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/data-Bakal2007.Rd:29: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/exportPAN.Rd:8: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/exportPAN.Rd:8: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/exportPAN.Rd:31: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/fitBM.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/fitNULL.Rd:25: file link 'dbeta' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/permNULL.Rd:28: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewNestedModules.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewNestedModules.Rd:38: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:10: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:28: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:42: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:60: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PANR.Rcheck/00install.out' for details.
* 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 ... NOTE
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for 'runif'
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for 'pbeta'
p2SNR,BetaMixture-numeric_Or_integer: no visible global function
  definition for 'qbeta'
Undefined global functions or variables:
  pbeta qbeta runif
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif")
to your NAMESPACE file.
* 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
fitNULL 31.34   0.28   31.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
fitNULL   26   0.17   26.23
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/PANR.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/PANR_1.29.1.tar.gz && rm -rf PANR.buildbin-libdir && mkdir PANR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PANR.buildbin-libdir PANR_1.29.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PANR_1.29.1.zip && rm PANR_1.29.1.tar.gz PANR_1.29.1.zip
###
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install for i386

* installing *source* package 'PANR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PANR'
    finding HTML links ... done
    BetaMixture-class                       html  
    PAN-class                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:21: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:85: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:85: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:89: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/PAN-class.Rd:89: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
    SNR2p                                   html  
    assoScore                               html  
    buildPAN                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:9: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/buildPAN.Rd:44: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    cosineSim                               html  
    data-Bakal2007                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/data-Bakal2007.Rd:29: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    edgeWeight                              html  
    exportPAN                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/exportPAN.Rd:8: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/exportPAN.Rd:8: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/exportPAN.Rd:31: file link 'write.graph' in package 'igraph' does not exist and so has been treated as a topic
    fitBM                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/fitBM.Rd:40: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    fitNULL                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/fitNULL.Rd:25: file link 'dbeta' in package 'stats' does not exist and so has been treated as a topic
    infer                                   html  
    p2SNR                                   html  
    permNULL                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/permNULL.Rd:28: file link 'BetaMixture' in package 'PANR' does not exist and so has been treated as a topic
    pvclustModule                           html  
    sigModules                              html  
    summarize                               html  
    view                                    html  
    viewLegend                              html  
    viewNestedModules                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewNestedModules.Rd:9: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewNestedModules.Rd:38: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
    viewPAN                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:10: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:28: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:42: file link 'RedeR' in package 'RedeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpWOq6J0/R.INSTALL19007f5037b9/PANR/man/viewPAN.Rd:60: file link 'layout' in package 'igraph' does not exist and so has been treated as a topic
** 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 'PANR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PANR' as PANR_1.29.1.zip
* DONE (PANR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PANR' successfully unpacked and MD5 sums checked

CHECK report for PANR on tokay2

Summary

Command output

Installation output

Tests output

Example timings