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CHECK report for seqplots on tokay1

This page was generated on 2021-05-06 12:33:34 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the seqplots package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1684/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqplots 1.28.0  (landing page)
Przemyslaw Stempor
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/seqplots
Branch: RELEASE_3_12
Last Commit: d3b50e7
Last Changed Date: 2020-10-27 10:58:50 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: seqplots
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqplots.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings seqplots_1.28.0.tar.gz
StartedAt: 2021-05-06 06:53:24 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:01:32 -0400 (Thu, 06 May 2021)
EllapsedTime: 488.0 seconds
RetCode: 1
Status:   ERROR   
CheckDir: seqplots.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqplots.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings seqplots_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/seqplots.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.28.0'
* 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 'seqplots' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/seqplots/man/plot.Rd:25: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/meat/seqplots.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 11.4Mb
  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
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 ... OK
* 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' ... ERROR
Running examples in 'seqplots-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPlotSetArray
> ### Title: Process genomic signal
> ### Aliases: getPlotSetArray
> 
> ### ** Examples
> 
>   
> # Get the paths of example files                      
> bed1 <- system.file("extdata", 
+     "Transcripts_ce10_chrI_100Kb.bed", package="seqplots")
> bed2 <- system.file("extdata", 
+     "GSM1208361_chrI_100Kb_PeakCalls.bed", package="seqplots")
> bw1 <- system.file("extdata", 
+     "GSM1208360_chrI_100Kb_q5_sample.bw", package="seqplots")
> 
> #If required install C. elegans genomic package from Bioconductor
> if(!"BSgenome.Celegans.UCSC.ce10" %in% BSgenome::installed.genomes()) {
+     if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
+         if (!requireNamespace("BiocManager", quietly=TRUE))
+         install.packages("BiocManager")
+         BiocManager::install("BSgenome.Celegans.UCSC.ce10")
+     }
+ }
> 
> #Get getPlotSetArray for track and feature files
> #Does not work on Windows i386 (32 bit)
> if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
+     plotset1 <- getPlotSetArray(bw1, c(bed1, bed2), 'ce10')
+ } else {
+     load(system.file("extdata", "precalc_plotset.Rdata", package="seqplots"))
+ }
Error in getREF(genome_ind) : No genomes installed!
Calls: getPlotSetArray -> getREF
Execution halted
* 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'
 ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  Error: No genomes installed!
  Backtrace:
      x
   1. \-seqplots::getPlotSetArray(bw1, c(bed1, bed2), "ce10") test1.R:22:8
   2.   \-seqplots::getREF(genome_ind)
  -- Error (test1.R:111:9): Test motifs ------------------------------------------
  Error: No genomes installed!
  Backtrace:
      x
   1. \-seqplots::getPlotSetArray(ms, c(bed1, bed2), "ce10") test1.R:111:8
   2.   \-seqplots::getREF(genome_ind)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 7 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/seqplots.Rcheck/00check.log'
for details.

Installation output

seqplots.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/seqplots_1.28.0.tar.gz && rm -rf seqplots.buildbin-libdir && mkdir seqplots.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqplots.buildbin-libdir seqplots_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL seqplots_1.28.0.zip && rm seqplots_1.28.0.tar.gz seqplots_1.28.0.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
100 4855k  100 4855k    0     0  25.5M      0 --:--:-- --:--:-- --:--:-- 25.7M

install for i386

* installing *source* package 'seqplots' ...
** using staged installation
** 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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/seqplots/man/plot.Rd:25: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    plotAverage                             html  
    plotHeatmap                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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-3.12-bioc/tmpdir/RtmpA9KbwF/R.INSTALL1ba84f37f14/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 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 'seqplots' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqplots' as seqplots_1.28.0.zip
* DONE (seqplots)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'seqplots' successfully unpacked and MD5 sums checked

Tests output

seqplots.Rcheck/tests_i386/test-all.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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')
== Skipped tests ===============================================================
* Skipping on Win 32bit (2)
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
  24.12    2.64   28.32

seqplots.Rcheck/tests_x64/test-all.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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')
== Skipped tests ===============================================================
* empty test (1)

== Failed tests ================================================================
-- Error (test1.R:22:9): Test getPlotSetArray function and plotting interfaces --
Error: No genomes installed!
Backtrace:
    x
 1. \-seqplots::getPlotSetArray(bw1, c(bed1, bed2), "ce10") test1.R:22:8
 2.   \-seqplots::getREF(genome_ind)
-- Error (test1.R:111:9): Test motifs ------------------------------------------
Error: No genomes installed!
Backtrace:
    x
 1. \-seqplots::getPlotSetArray(ms, c(bed1, bed2), "ce10") test1.R:111:8
 2.   \-seqplots::getREF(genome_ind)

[ FAIL 2 | WARN 0 | SKIP 1 | PASS 7 ]
Error: Test failures
Execution halted

Example timings

seqplots.Rcheck/examples_i386/seqplots-Ex.timings

nameusersystemelapsed
MotifSetup-class0.030.000.03
getPlotSetArray2.080.712.80
plot0.500.060.56
plotAverage0.090.010.11
plotHeatmap0.220.000.22
run000

seqplots.Rcheck/examples_x64/seqplots-Ex.timings

nameusersystemelapsed
MotifSetup-class0.080.000.08