Hello everyone,
I would like to automagically install an R package when installing my
tool. So I wrote this in my "tool_dependencies.xml":
---
<package name="R_PACKAGES" version="1.0">
<install version="1.0">
<actions>
<action type="shell_command">R --slave
--no-save --no-restore --quiet -e 'if("Hmisc" %in%
rownames(installed.packages()) == FALSE){install.packages("Hmisc",
repos = c("http://cran.rstudio.com/";), dependencies = TRUE)}'</action>
</actions>
</install>
</package>
---
This does not seem to work and the problem is:
---
/bin/sh: 1: cd: can't cd to ./database/tmp/tmpI6RcEu/R_PACKAGES
---
What is true is that I have this in the Galaxy log:
---
Warning: local() encountered an error (return code 2) while executing 'R
--slave --no-save --no-restore --quiet -e 'if("Hmisc" %in%
rownames(installed.packages()) == FALSE){install.packages("Hmisc",
repos = c("http://cran.rstudio.com/";), dependencies = TRUE)}''
[localhost] local: rm -rf ./database/tmp/tmpI6RcEu
---
I do not think that the local error is related (I have it everywhere), but
a premature "rm -rf ./database/tmp/tmpI6RcEu" might explain the problem. I
tried another install (e.g. package_samtools_0_1_16), which downloads and
makes the samtools: no problem.
Does anyone have a suggestion?
Many thanks,
Matthias.
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