usegalaxy-playbook
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galaxyproject
Scatterplot w ggplot2 (Galaxy Version 2.2.1+galaxy1) fails at usegalaxy.org
Problem: Seems to be an install or configuration issue? Reliably fails at usegalaxy.org, is fine at usegalaxy.eu.
This tool is part of the "Galaxy 101 for Everyone" tutorial. Does not show up in "tool likely broken" queries -- probably not executed enough (checked 1 & 2 weeks prior), but we have 3 bug reports about it. And I could reproduce it.
Notes:
It isn't a data problem -- I checked that a few different ways. Also checked different parameter levels. No pattern, all fail the same way.
Also -- I'm not sure that having csv datasets display as tabular is helpful, or if that was on purpose. If you change the datatype for a csv dataset to tabular then it displays as csv would plain text. Kinda the reverse of I was expecting, and not so helpful for new users. If that display is not on purpose -- lmk and can open a distinct bug report against /galaxy. The same display behavior is in every Galaxy I've checked (local, org, other public Galaxy).
Tests:
- https://usegalaxy.org/u/jen/h/test-101-for-everybody
- https://usegalaxy.eu/u/jenj/h/test-101-for-everybody
Error messages:
stderr
Error in alpha * 255 : non-numeric argument to binary operator Calls: ggsave ... validGP -> numnotnull -> alpha -> <Anonymous> -> encode_c
stdout
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")library(ggplot2)
#Choose between automatically scaled x and y axis or user defined gg_scalex = NULL gg_scaley = NULL gg_theme = theme_bw() gg_legend = theme(legend.position="right")input <- read.csv('/galaxy-repl/main/files/039/791/dataset_39791479.dat', sep='\t', header=TRUE)
names(input)[1] <- "xcol" names(input)[2] <- "ycol"
gg_facet = NULL gg_factor = aes(colour=factor(factor)) gg_point = geom_point(size=2.0, alpha='1.0', gg_factor) gg_line = geom_line(size=2.0, alpha='1.0', gg_factor) color_scale = scale_color_brewer(palette='Set2', direction='1') names(input)[5] <- "factor" gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL)) gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL)) gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL)) gg_gridline = NULL gg_line = NULL#this is the actual ggplot command to make the final plot(s) plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet + gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('Sepal length as a function of sepal width') + xlab('Sepal length') + ylab('Sepal width')+ gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
gg_width <- as.double('7.0') gg_height <- as.double('7.0') gg_unit <- 'in' gg_dpi <- as.double('300.0') gg_add_device <- 'pdf' output1 <- '/galaxy-repl/main/files/039/791/dataset_39791719.dat' output2 <- '/galaxy-repl/main/files/039/791/dataset_39791720.dat' ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png") if(gg_add_device != "none"){ ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device) }
job info (first lines from stdout and what displays in the red error dataset in the history)
options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")library(ggplot2)
#Choose between automatically scaled x and y axis or user defi
bug report info
Dataset Error An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1.
Error Details Execution resulted in the following messages:
Fatal error: Exit code 1 () Tool generated the following standard error:
Error in alpha * 255 : non-numeric argument to binary operator Calls: ggsave ... validGP -> numnotnull -> alpha -> <Anonymous> -> encode_c
ping @natefoo @davebx @mvdbeek
@bgruening Would you mind getting a conda list of your mulled-v1-3ed3a1ca990ccd31d8603d426d444c25343ad90a8f7378000926d72f8a90a339 env?
# packages in environment at /usr/local/tools/_conda/envs/mulled-v1-3ed3a1ca990ccd31d8603d426d444c25343ad90a8f7378000926d72f8a90a339:
#
# Name Version Build Channel
bzip2 1.0.6 h470a237_2 conda-forge
ca-certificates 2018.4.16 0 conda-forge
cairo 1.14.6 4 conda-forge
curl 7.54.1 0 conda-forge
fontconfig 2.12.1 6 conda-forge
freetype 2.7 1 conda-forge
gettext 0.19.8.1 0 conda-forge
glib 2.51.4 0 conda-forge
graphite2 1.3.11 hfc679d8_0 conda-forge
gsl 2.1 2 conda-forge
harfbuzz 1.4.3 0 conda-forge
icu 58.2 hfc679d8_0 conda-forge
jpeg 9c h470a237_0 conda-forge
krb5 1.14.6 0 conda-forge
libffi 3.2.1 3 conda-forge
libgcc 7.2.0 h69d50b8_2
libgcc-ng 7.2.0 hdf63c60_3
libiconv 1.15 h470a237_1 conda-forge
libpng 1.6.28 1 conda-forge
libssh2 1.8.0 1 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3
libtiff 4.0.7 0 conda-forge
libxcb 1.13 h470a237_2 conda-forge
libxml2 2.9.5 0 conda-forge
ncurses 5.9 10 conda-forge
openssl 1.0.2o h470a237_1 conda-forge
pango 1.40.4 0 conda-forge
pcre 8.41 h470a237_2 conda-forge
pixman 0.34.0 2 conda-forge
pthread-stubs 0.4 h470a237_1 conda-forge
r-assertthat 0.2.0 r3.3.2_0 conda-forge
r-base 3.3.2 5 conda-forge
r-colorspace 1.3_2 r3.3.2_0 conda-forge
r-dichromat 2.0_0 r3.3.2_0 conda-forge
r-digest 0.6.12 r3.3.2_0 bioconda
r-gdtools 0.1.4 r3.3.2_0 bioconda
r-ggplot2 2.2.1 r3.3.2_0 bioconda
r-gtable 0.2.0 r3.3.2_0 conda-forge
r-labeling 0.3 r3.3.2_0 conda-forge
r-lazyeval 0.2.1 r3.3.2_0 conda-forge
r-magrittr 1.5 r3.3.2_0 conda-forge
r-mass 7.3_48 r3.3.2_0 conda-forge
r-munsell 0.4.3 r3.3.2_0 conda-forge
r-plyr 1.8.4 r3.3.2_0 conda-forge
r-rcolorbrewer 1.1_2 r3.3.2_0 conda-forge
r-rcpp 0.12.16 r3.3.2_0 conda-forge
r-reshape2 1.4.3 r3.3.2_0 conda-forge
r-scales 0.4.1 r3.3.2_1 bioconda
r-stringi 1.1.7 r3.3.2_1 conda-forge
r-stringr 1.2.0 r3.3.2_0 conda-forge
r-svglite 1.2.1 r3.3.2_0 conda-forge
r-tibble 1.2 r3.3.2_1 bioconda
r-withr 2.1.1 r3.3.2_0 conda-forge
readline 6.2 0 conda-forge
tk 8.5.19 2 conda-forge
xorg-kbproto 1.0.7 h470a237_2 conda-forge
xorg-libx11 1.6.5 h470a237_2 conda-forge
xorg-libxau 1.0.8 h470a237_6 conda-forge
xorg-libxdmcp 1.1.2 h470a237_7 conda-forge
xorg-libxext 1.3.3 h470a237_4 conda-forge
xorg-libxrender 0.9.10 h470a237_2 conda-forge
xorg-renderproto 0.11.1 h470a237_2 conda-forge
xorg-xextproto 7.3.0 h470a237_2 conda-forge
xorg-xproto 7.0.31 h470a237_7 conda-forge
xz 5.2.4 h470a237_0 conda-forge
zlib 1.2.8 3 conda-forge
(mulled-v1-3ed3a1ca990ccd31d8603d426d444c25343ad90a8f7378000926d72f8a90a339) galaxy@sn04:~$
and this should make your life easier:
name: mulled-v1-3ed3a1ca990ccd31d8603d426d444c25343ad90a8f7378000926d72f8a90a339
channels:
- iuc
- conda-forge
- bioconda
- defaults
- bgruening
dependencies:
- bzip2=1.0.6=h470a237_2
- ca-certificates=2018.4.16=0
- cairo=1.14.6=4
- curl=7.54.1=0
- fontconfig=2.12.1=6
- freetype=2.7=1
- gettext=0.19.8.1=0
- glib=2.51.4=0
- graphite2=1.3.11=hfc679d8_0
- gsl=2.1=2
- harfbuzz=1.4.3=0
- icu=58.2=hfc679d8_0
- jpeg=9c=h470a237_0
- krb5=1.14.6=0
- libffi=3.2.1=3
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=7.2.0=hdf63c60_3
- libiconv=1.15=h470a237_1
- libpng=1.6.28=1
- libssh2=1.8.0=1
- libstdcxx-ng=7.2.0=hdf63c60_3
- libtiff=4.0.7=0
- libxcb=1.13=h470a237_2
- libxml2=2.9.5=0
- ncurses=5.9=10
- openssl=1.0.2o=h470a237_1
- pango=1.40.4=0
- pcre=8.41=h470a237_2
- pixman=0.34.0=2
- pthread-stubs=0.4=h470a237_1
- r-assertthat=0.2.0=r3.3.2_0
- r-base=3.3.2=5
- r-colorspace=1.3_2=r3.3.2_0
- r-dichromat=2.0_0=r3.3.2_0
- r-digest=0.6.12=r3.3.2_0
- r-gdtools=0.1.4=r3.3.2_0
- r-ggplot2=2.2.1=r3.3.2_0
- r-gtable=0.2.0=r3.3.2_0
- r-labeling=0.3=r3.3.2_0
- r-lazyeval=0.2.1=r3.3.2_0
- r-magrittr=1.5=r3.3.2_0
- r-mass=7.3_48=r3.3.2_0
- r-munsell=0.4.3=r3.3.2_0
- r-plyr=1.8.4=r3.3.2_0
- r-rcolorbrewer=1.1_2=r3.3.2_0
- r-rcpp=0.12.16=r3.3.2_0
- r-reshape2=1.4.3=r3.3.2_0
- r-scales=0.4.1=r3.3.2_1
- r-stringi=1.1.7=r3.3.2_1
- r-stringr=1.2.0=r3.3.2_0
- r-svglite=1.2.1=r3.3.2_0
- r-tibble=1.2=r3.3.2_1
- r-withr=2.1.1=r3.3.2_0
- readline=6.2=0
- tk=8.5.19=2
- xorg-kbproto=1.0.7=h470a237_2
- xorg-libx11=1.6.5=h470a237_2
- xorg-libxau=1.0.8=h470a237_6
- xorg-libxdmcp=1.1.2=h470a237_7
- xorg-libxext=1.3.3=h470a237_4
- xorg-libxrender=0.9.10=h470a237_2
- xorg-renderproto=0.11.1=h470a237_2
- xorg-xextproto=7.3.0=h470a237_2
- xorg-xproto=7.0.31=h470a237_7
- xz=5.2.4=h470a237_0
- zlib=1.2.8=3
prefix: /usr/local/tools/_conda/envs/mulled-v1-3ed3a1ca990ccd31d8603d426d444c25343ad90a8f7378000926d72f8a90a339