Package: seqplots

Version: 1.20.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqplots.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings seqplots_1.20.1.tar.gz

StartedAt: 2019-04-13 05:26:29 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:33:12 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 403.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: seqplots.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqplots.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings seqplots_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/seqplots.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 'seqplots/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seqplots' version '1.20.1'
* 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 'seqplots' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/getPlotSetArray.Rd:144: file link 'installed.genomes' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/getPlotSetArray.Rd:147: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/ggHeatmapPlotWrapper.Rd:75: file link 'grDevices' in package 'grDevices' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/heatmapPlotWrapper.Rd:76: file link 'grDevices' in package 'grDevices' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/plotHeatmap.Rd:177: file link 'grDevices' in package 'grDevices' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/plotHeatmap.Rd:192: file link 'geom_raster' in package 'ggplot2' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/seqplots.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    seqplots  10.2Mb
* 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
Namespace in Imports field not imported from: 'BiocManager'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
import.narrowPeak: warning in import(x, forma = "bed", extraCols =
  extraCols): partial argument match of 'forma' to 'format'
add_local_file: no visible global function definition for
  'doFileOperations'
getPlotSetArray : <anonymous>: no visible global function definition
  for 'qt'
getSF : <anonymous>: no visible global function definition for 'approx'
ggHeatmapPlotWrapper: no visible global function definition for
  'colorRampPalette'
ggHeatmapPlotWrapper: no visible binding for global variable 'Var2'
ggHeatmapPlotWrapper: no visible binding for global variable 'Var1'
ggHeatmapPlotWrapper: no visible binding for global variable 'value'
heatmapPlotWrapper: no visible global function definition for
  'colorRampPalette'
heatmapPlotWrapper: no visible global function definition for 'layout'
heatmapPlotWrapper: no visible global function definition for
  'capture.output'
heatmapPlotWrapper: no visible global function definition for 'par'
heatmapPlotWrapper: no visible global function definition for 'abline'
heatmapPlotWrapper: no visible global function definition for 'axis'
heatmapPlotWrapper: no visible global function definition for 'image'
heatmapPlotWrapper: no visible global function definition for 'rect'
heatmapPlotWrapper: no visible global function definition for
  'plot.new'
heatmapPlotWrapper: no visible global function definition for 'text'
heatmapPlotWrapper: no visible global function definition for 'title'
heatmapPlotWrapper: no visible global function definition for 'box'
imPlot2: no visible global function definition for 'par'
imPlot2: no visible global function definition for 'image'
imPlot2: no visible global function definition for 'rect'
imPlot2: no visible global function definition for 'axis'
imPlot2: no visible global function definition for 'box'
imPlot2: no visible binding for global variable 'mtext'
plotMext: no visible global function definition for 'par'
plotMext: no visible global function definition for 'rainbow'
plotMext: no visible global function definition for 'plot.new'
plotMext: no visible global function definition for 'rgb'
plotMext: no visible global function definition for 'text'
plotMext: no visible global function definition for 'axis'
plotMext: no visible global function definition for 'adjustcolor'
plotMext: no visible global function definition for 'lines'
plotMext: no visible global function definition for 'abline'
plotAverage,list: no visible global function definition for 'par'
plotHeatmap,list: no visible global function definition for 'par'
plotHeatmap,list: no visible global function definition for 'plot.new'
plotHeatmap,list: no visible global function definition for 'text'
plotHeatmap,list: no visible global function definition for 'kmeans'
plotHeatmap,list: no visible global function definition for 'hclust'
plotHeatmap,list: no visible global function definition for 'dist'
plotHeatmap,list: no visible global function definition for 'cutree'
plotHeatmap,list: no visible global function definition for
  'as.dendrogram'
plotHeatmap,list: no visible global function definition for 'title'
Undefined global functions or variables:
  Var1 Var2 abline adjustcolor approx as.dendrogram axis box
  capture.output colorRampPalette cutree dist doFileOperations hclust
  image kmeans layout lines mtext par plot.new qt rainbow rect rgb text
  title value
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow",
             "rgb")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "mtext", "par", "plot.new", "rect", "text",
             "title")
  importFrom("stats", "approx", "as.dendrogram", "cutree", "dist",
             "hclust", "kmeans", "qt")
  importFrom("utils", "capture.output")
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 ... WARNING
Undocumented arguments in documentation object 'plotHeatmap'
  'plotz' 'FO' 'CL' 'sort_by' 'sort_mids' 'sort_dst' 'clst_mids'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getPlotSetArray 5.69   0.79    6.57
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 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 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/seqplots.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/seqplots_1.20.1.tar.gz && rm -rf seqplots.buildbin-libdir && mkdir seqplots.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqplots.buildbin-libdir seqplots_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL seqplots_1.20.1.zip && rm seqplots_1.20.1.tar.gz seqplots_1.20.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 20 4854k   20 1008k    0     0  12.7M      0 --:--:-- --:--:-- --:--:-- 13.3M
100 4854k  100 4854k    0     0  42.0M      0 --:--:-- --:--:-- --:--:-- 43.1M

install for i386

* installing *source* package 'seqplots' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'seqplots'
    finding HTML links ... done
    MotifSetup-class                        html  
    PlotSetArray-class                      html  
    PlotSetList-class                       html  
    PlotSetPair-class                       html  
    add_local_file                          html  
    deployServerInstance                    html  
    getPlotSetArray                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/getPlotSetArray.Rd:144: file link 'installed.genomes' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/getPlotSetArray.Rd:147: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    getREF                                  html  
    ggHeatmapPlotWrapper                    html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/ggHeatmapPlotWrapper.Rd:75: file link 'grDevices' in package 'grDevices' does not exist and so has been treated as a topic
    heatmapPlotWrapper                      html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/heatmapPlotWrapper.Rd:76: file link 'grDevices' in package 'grDevices' does not exist and so has been treated as a topic
    imPlot2                                 html  
    import.narrowPeak                       html  
    num2bp                                  html  
    num2sci                                 html  
    plot                                    html  
    plotAverage                             html  
    plotHeatmap                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/plotHeatmap.Rd:177: file link 'grDevices' in package 'grDevices' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpe0xJOv/R.INSTALL20c041a768d/seqplots/man/plotHeatmap.Rd:192: file link 'geom_raster' in package 'ggplot2' does not exist and so has been treated as a topic
    plotMext                                html  
    run                                     html  
    seqplots-generic                        html  
    seqplots                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'seqplots' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqplots' as seqplots_1.20.1.zip
* DONE (seqplots)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'seqplots' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(seqplots)
SeqPlots ready, type "run()" to start web interface (GUI) or "?getPlotSetArray" for console mode help.
> 
> message('Runing only command line tests, skipping GUI')
Runing only command line tests, skipping GUI
> test_check("seqplots", filter='1')
== testthat results  ===========================================================
OK: 44 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.68    1.42   15.09 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(seqplots)
SeqPlots ready, type "run()" to start web interface (GUI) or "?getPlotSetArray" for console mode help.
> 
> message('Runing only command line tests, skipping GUI')
Runing only command line tests, skipping GUI
> test_check("seqplots", filter='1')
PlotSetPair contatining: GSM1208360_chrI_100Kb_q5_sample @ Transcripts_ce10_chrI_100Kb== testthat results  ===========================================================
OK: 54 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  24.46    1.12   25.59