Package: cogena

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cogena.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cogena_1.16.0.tar.gz

StartedAt: 2019-04-13 01:23:52 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:31:29 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 457.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cogena.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cogena.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cogena_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cogena.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 'cogena/DESCRIPTION' ... OK
* this is package 'cogena' version '1.16.0'
* package encoding: UTF-8
* 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 'cogena' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cogena.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
dist.fn: no visible global function definition for 'cor'
heatmap.3: no visible binding for global variable 'dist'
heatmap.3: no visible global function definition for 'par'
heatmap.3: no visible global function definition for 'median'
heatmap.3: no visible global function definition for 'order.dendrogram'
heatmap.3: no visible global function definition for 'reorder'
heatmap.3: no visible binding for global variable 'sd'
heatmap.3: no visible global function definition for 'layout'
heatmap.3: no visible global function definition for 'image'
heatmap.3: no visible global function definition for 'axis'
heatmap.3: no visible global function definition for 'mtext'
heatmap.3: no visible global function definition for 'rect'
heatmap.3: no visible global function definition for 'abline'
heatmap.3: no visible global function definition for 'lines'
heatmap.3: no visible global function definition for 'text'
heatmap.3: no visible global function definition for 'plot.new'
heatmap.3: no visible global function definition for 'title'
heatmap.3: no visible global function definition for 'density'
heatmap.3: no visible global function definition for 'hist'
plot.sota: no visible global function definition for 'par'
corInCluster,cogena: no visible global function definition for 'cor'
heatmapCluster,cogena: no visible global function definition for
  'topo.colors'
heatmapCluster,cogena: no visible global function definition for
  'rainbow'
heatmapCluster,cogena: no visible global function definition for 'par'
heatmapCluster,cogena: no visible global function definition for
  'legend'
Undefined global functions or variables:
  abline axis cor density dist hist image layout legend lines median
  mtext order.dendrogram par plot.new rainbow rect reorder sd text
  title topo.colors
Consider adding
  importFrom("grDevices", "rainbow", "topo.colors")
  importFrom("graphics", "abline", "axis", "hist", "image", "layout",
             "legend", "lines", "mtext", "par", "plot.new", "rect",
             "text", "title")
  importFrom("stats", "cor", "density", "dist", "median",
             "order.dendrogram", "reorder", "sd")
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
cogena_package 6.28   0.99   83.17
clEnrich_one   3.39   0.14   12.19
clEnrich       2.69   0.17   16.80
upDownGene     2.56   0.13   17.96
clusterMethods 1.37   0.01    7.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cogena_package 4.22   0.41   90.57
clEnrich_one   2.78   0.16   12.01
clEnrich       2.34   0.17   15.64
upDownGene     1.75   0.20   16.19
clusterMethods 1.25   0.03    9.58
* 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-3.8-bioc/meat/cogena.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/cogena_1.16.0.tar.gz && rm -rf cogena.buildbin-libdir && mkdir cogena.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cogena.buildbin-libdir cogena_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cogena_1.16.0.zip && rm cogena_1.16.0.tar.gz cogena_1.16.0.zip
###
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install for i386

* installing *source* package 'cogena' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
** help
*** installing help indices
  converting help for package 'cogena'
    finding HTML links ... done
    AllGeneSymbols                          html  
    DEexprs                                 html  
    PEI                                     html  
    Psoriasis                               html  
    clEnrich                                html  
    clEnrich_one                            html  
    clusterMethods                          html  
    coExp                                   html  
    cogena_class                            html  
    cogena_package                          html  
    corInCluster                            html  
    enrichment                              html  
    gene2set                                html  
    geneExpInCluster                        html  
    geneInCluster                           html  
    genecl_class                            html  
    geneclusters                            html  
    gmt2list                                html  
    gmtlist2file                            html  
    heatmap.3                               html  
    heatmapCluster                          html  
    heatmapCmap                             html  
    heatmapPEI                              html  
    mat                                     html  
    nClusters                               html  
    pClusters                               html  
    sampleLabel                             html  
    show                                    html  
    sota                                    html  
    summary                                 html  
    upDownGene                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
In R CMD INSTALL

install for x64

* installing *source* package 'cogena' ...
** testing if installed package can be loaded
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
* MD5 sums
packaged installation of 'cogena' as cogena_1.16.0.zip
* DONE (cogena)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cogena' successfully unpacked and MD5 sums checked
In R CMD INSTALL