Package: BioTIP

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioTIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BioTIP_1.0.0.tar.gz

StartedAt: 2020-04-15 01:39:05 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:41:05 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 119.8 seconds

RetCode: 0

Status:  OK

CheckDir: BioTIP.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioTIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BioTIP_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/BioTIP.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioTIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioTIP' version '1.0.0'
* package encoding: UTF-8
* 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 'BioTIP' 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 ... NOTE
getCluster: warning in cluster_walktrap(igraphL[[i]], weight =
  abs(E(igraphL[[i]])$weight), steps = steps[i]): partial argument
  match of 'weight' to 'weights'
getBiotypes: no visible global function definition for 'is'
getBiotypes: no visible global function definition for 'queryHits'
getBiotypes: no visible global function definition for 'subjectHits'
getBiotypes: no visible global function definition for 'aggregate'
getCI_inner : <anonymous>: no visible global function definition for
  'cor'
getCI_inner : <anonymous>: no visible binding for global variable 'sd'
getCluster_methods : <anonymous>: no visible global function definition
  for 'hclust'
getCluster_methods : <anonymous>: no visible global function definition
  for 'dist'
getCluster_methods: no visible global function definition for 'par'
getCluster_methods : <anonymous>: no visible global function definition
  for 'plot'
getCluster_methods : <anonymous>: no visible global function definition
  for 'cutree'
getIc : <anonymous>: no visible global function definition for 'cor'
getMCI : <anonymous>: no visible global function definition for 'cor'
getMCI : <anonymous>: no visible binding for global variable 'sd'
getNetwork: no visible global function definition for 'stack'
getReadthrough: no visible global function definition for 'subjectHits'
getReadthrough: no visible binding for global variable 'readthrough'
getReadthrough : <anonymous>: no visible global function definition for
  'queryHits'
getReadthrough : <anonymous>: no visible global function definition for
  'subjectHits'
optimize.sd_selection : <anonymous>: no visible binding for global
  variable 'sd'
optimize.sd_selection: no visible binding for global variable 'sd'
optimize.sd_selection : <anonymous> : <anonymous>: no visible global
  function definition for 'sd'
plotBar_MCI: no visible global function definition for 'par'
plotBar_MCI: no visible global function definition for 'barplot'
plotBar_MCI: no visible global function definition for 'rainbow'
plotBar_MCI: no visible global function definition for 'text'
plotIc: no visible global function definition for 'matplot'
plotIc: no visible global function definition for 'axis'
plotMaxMCI: no visible global function definition for 'is'
plotMaxMCI: no visible global function definition for 'matplot'
plotMaxMCI: no visible global function definition for 'text'
plotMaxMCI: no visible global function definition for 'axis'
plot_Ic_Simulation: no visible global function definition for 'matplot'
plot_Ic_Simulation: no visible global function definition for 'axis'
plot_MCI_Simulation: no visible global function definition for
  'boxplot'
plot_MCI_Simulation: no visible global function definition for 'axis'
plot_MCI_Simulation: no visible global function definition for 'points'
plot_simulation_sample: no visible global function definition for
  'density'
plot_simulation_sample: no visible global function definition for
  'plot'
plot_simulation_sample: no visible global function definition for
  'abline'
plot_simulation_sample: no visible global function definition for
  'text'
sd_selection : <anonymous>: no visible binding for global variable 'sd'
sd_selection: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline aggregate axis barplot boxplot cor cutree density dist hclust
  is matplot par plot points queryHits rainbow readthrough sd stack
  subjectHits text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot",
             "matplot", "par", "plot", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "aggregate", "cor", "cutree", "density", "dist",
             "hclust", "sd")
  importFrom("utils", "stack")
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 ... NOTE
  Note: found 15 marked UTF-8 strings
* 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-3.10-bioc/meat/BioTIP.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/BioTIP_1.0.0.tar.gz && rm -rf BioTIP.buildbin-libdir && mkdir BioTIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioTIP.buildbin-libdir BioTIP_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BioTIP_1.0.0.zip && rm BioTIP_1.0.0.tar.gz BioTIP_1.0.0.zip
###
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install for i386

* installing *source* package 'BioTIP' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioTIP'
    finding HTML links ... done
    BioTIP-package                          html  
    GSE6136_cli                             html  
    GSE6136_matrix                          html  
    ILEF                                    html  
    cod                                     html  
    gencode                                 html  
    getBiotypes                             html  
    getCTS                                  html  
    getCluster_methods                      html  
    getIc                                   html  
    getMCI                                  html  
    finding level-2 HTML links ... done

    getMaxMCImember                         html  
    getMaxStats                             html  
    getNetwork                              html  
    getReadthrough                          html  
    intron                                  html  
    optimize.sd_selection                   html  
    plotBar_MCI                             html  
    plotIc                                  html  
    plotMaxMCI                              html  
    plot_Ic_Simulation                      html  
    plot_MCI_Simulation                     html  
    plot_simulation_sample                  html  
    sd_selection                            html  
    simulationMCI                           html  
    simulation_Ic                           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 'BioTIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioTIP' as BioTIP_1.0.0.zip
* DONE (BioTIP)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'BioTIP' successfully unpacked and MD5 sums checked