| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q R [S] T U V W X Y Z |
This page was generated on 2017-04-15 16:19:07 -0400 (Sat, 15 Apr 2017).
| Package 1130/1296 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| seqplots 1.12.0 Przemyslaw Stempor
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: seqplots |
| Version: 1.12.0 |
| Command: rm -rf seqplots.buildbin-libdir seqplots.Rcheck && mkdir seqplots.buildbin-libdir seqplots.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=seqplots.buildbin-libdir seqplots_1.12.0.tar.gz >seqplots.Rcheck\00install.out 2>&1 && cp seqplots.Rcheck\00install.out seqplots-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=seqplots.buildbin-libdir --install="check:seqplots-install.out" --force-multiarch --no-vignettes --timings seqplots_1.12.0.tar.gz |
| StartedAt: 2017-04-15 00:47:21 -0400 (Sat, 15 Apr 2017) |
| EndedAt: 2017-04-15 00:52:43 -0400 (Sat, 15 Apr 2017) |
| EllapsedTime: 322.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: seqplots.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf seqplots.buildbin-libdir seqplots.Rcheck && mkdir seqplots.buildbin-libdir seqplots.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=seqplots.buildbin-libdir seqplots_1.12.0.tar.gz >seqplots.Rcheck\00install.out 2>&1 && cp seqplots.Rcheck\00install.out seqplots-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=seqplots.buildbin-libdir --install="check:seqplots-install.out" --force-multiarch --no-vignettes --timings seqplots_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/seqplots.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.12.0'
* 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 ... OK
* checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
doc 2.4Mb
seqplots 4.8Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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
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 'title'
heatmapPlotWrapper: no visible global function definition for 'box'
heatmapPlotWrapper: no visible global function definition for
'plot.new'
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 '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 '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: possible error in supersom(Hlist, grid =
class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"), rlen =
100, toroidal = TRUE): unused argument (toroidal = TRUE)
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 hclust image kmeans
layout lines mtext par plot.new qt rainbow rect rgb title value
Consider adding
importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow",
"rgb")
importFrom("graphics", "abline", "axis", "box", "image", "layout",
"lines", "mtext", "par", "plot.new", "rect", "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 installed files from 'inst/doc' ... 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386/R" CMD BATCH --vanilla "test-all.R" "test-all.Rout"' had status 1
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
7: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters,
clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend,
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
8: supersom(Hlist, grid = class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"),
rlen = 100, toroidal = TRUE)
testthat results ================================================================
OK: 42 SKIPPED: 1 FAILED: 1
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'test-all.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64/R" CMD BATCH --vanilla "test-all.R" "test-all.Rout"' had status 1
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
7: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters,
clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend,
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
8: supersom(Hlist, grid = class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"),
rlen = 100, toroidal = TRUE)
testthat results ================================================================
OK: 64 SKIPPED: 0 FAILED: 1
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53)
Error: testthat unit tests failed
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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/seqplots.Rcheck/00check.log'
for details.
test-all.Rout.fail:
R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 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')
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53) --
unused argument (toroidal = TRUE)
1: expect_is(plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing",
clstmethod = "ssom"), "data.frame") at testthat/test1.R:53
2: klass(object)
3: paste(class(x), collapse = "/")
4: plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing", clstmethod = "ssom")
5: plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing", clstmethod = "ssom")
6: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters,
clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend,
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
7: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters,
clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend,
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
8: supersom(Hlist, grid = class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"),
rlen = 100, toroidal = TRUE)
testthat results ================================================================
OK: 42 SKIPPED: 1 FAILED: 1
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53)
Error: testthat unit tests failed
Execution halted
test-all.Rout.fail:
R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(seqplots)
SeqPlots ready, type "run()" to start web interface (GUI) or "?getPlotSetArray" for console mode help.
>
> message('Runing only command line tests, skipping GUI')
Runing only command line tests, skipping GUI
> test_check("seqplots", filter='1')
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53) --
unused argument (toroidal = TRUE)
1: expect_is(plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing",
clstmethod = "ssom"), "data.frame") at testthat/test1.R:53
2: klass(object)
3: paste(class(x), collapse = "/")
4: plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing", clstmethod = "ssom")
5: plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing", clstmethod = "ssom")
6: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters,
clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend,
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
7: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters,
clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend,
xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec,
clspace, pointsize, embed, ggplot, raster, ...)
8: supersom(Hlist, grid = class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"),
rlen = 100, toroidal = TRUE)
testthat results ================================================================
OK: 64 SKIPPED: 0 FAILED: 1
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53)
Error: testthat unit tests failed
Execution halted
seqplots.Rcheck/00install.out:
install for i386 * installing *source* package 'seqplots' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'seqplots' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'seqplots' as seqplots_1.12.0.zip * DONE (seqplots)
seqplots.Rcheck/examples_i386/seqplots-Ex.timings:
| name | user | system | elapsed | |
| MotifSetup-class | 0.02 | 0.00 | 0.01 | |
| getPlotSetArray | 0.98 | 0.36 | 1.35 | |
| plot | 0.89 | 0.02 | 0.90 | |
| plotAverage | 0.07 | 0.00 | 0.07 | |
| plotHeatmap | 0.11 | 0.00 | 0.11 | |
| run | 0 | 0 | 0 | |
seqplots.Rcheck/examples_x64/seqplots-Ex.timings:
| name | user | system | elapsed | |
| MotifSetup-class | 0.02 | 0.00 | 0.02 | |
| getPlotSetArray | 3.98 | 0.38 | 4.41 | |
| plot | 0.80 | 0.00 | 0.79 | |
| plotAverage | 0.97 | 0.01 | 1.11 | |
| plotHeatmap | 1.04 | 0.07 | 1.11 | |
| run | 0 | 0 | 0 | |