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galaxyproject / usegalaxy-playbook

Ansible Playbook for usegalaxy.org
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Scatterplot w ggplot2 (Galaxy Version 2.2.1+galaxy1) fails at usegalaxy.org #298

Open jennaj opened 4 years ago

jennaj commented 4 years ago

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:

Error messages:

stderr

Error in alpha * 255 : non-numeric argument to binary operator Calls: ggsave ... validGP -> numnotnull -> alpha -> -> 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 -> -> encode_c

ping @natefoo @davebx @mvdbeek

natefoo commented 4 years ago

@bgruening Would you mind getting a conda list of your mulled-v1-3ed3a1ca990ccd31d8603d426d444c25343ad90a8f7378000926d72f8a90a339 env?

bgruening commented 4 years ago 
# 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:~$
bgruening commented 4 years ago

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