devtools install magic to install aggiedown

[ctb]

when snakemake creates a new conda env to build, it's not installing aggiedown for me.

to fix, I perform the following incantations:

• activate relevant conda environment
• change into a directory containing https://github.com/ryanpeek/aggiedown at ae99300d43b
• run R
• at the R console, run devtools::install(), and hit 3 (None) or 'enter' so as to not install anything other than aggiedown.

This installs the right version of aggiedown, AFAICT.

[luizirber]

I didn't get to create an aggiedown recipe for conda-forge yet, but there is a rule in the Snakefile to install it properly: snakemake --use-conda install_deps should work.

[ctb]

will try

[ctb]

Downloading GitHub repo ryanpeek/aggiedown@ae99300d43bdccc16069efcc08198624c76eee0c
sh: /bin/tar: No such file or directory
sh: /bin/tar: No such file or directory
Error in length(file_list) > 0 : error in running command
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning messages:
1: In system(paste(TAR, "--version >", tf, "2>&1")) :
  error in running command
2: In system(cmd) : error in running command
3: In utils::untar(tarfile, ...) :
  ‘/usr/bin/gzip -dc '/var/folders/y6/s1r3q87933s6gjdrtmts1npc0000gq/T//RtmpZn8NUJ/file1159e6e6d74f9.tar.gz' | /bin/tar -xf '-' -C '/var/folders/y6/s1r3q87933s6gjdrtmts1npc0000gq/T//RtmpZn8NUJ/remotes1159e541ac012'’ returned error code 127
4: In system(paste(TAR, "--version >", tf, "2>&1")) :
  error in running command
Execution halted

[luizirber]

Interesting... I add tar as a dependency in the R env, let's see if it works.

[ctb]

In addition: Warning messages:
1: In system(paste(TAR, "--version >", tf, "2>&1")) :
  error in running command
2: In system(cmd) : error in running command
3: In utils::untar(tarfile, ...) :
  ‘/usr/bin/gzip -dc '/var/folders/y6/s1r3q87933s6gjdrtmts1npc0000gq/T//Rtmpn6qsRs/file12d59398bc424.tar.gz' | /bin/tar -xf '-' -C '/var/folders/y6/s1r3q87933s6gjdrtmts1npc0000gq/T//Rtmpn6qsRs/remotes12d596fa3500'’ returned error code 127
4: In system(paste(TAR, "--version >", tf, "2>&1")) :
  error in running command
Execution halted

there's still no /bin/tar? is there a reason to use absolute paths here? or is that in someone else's code?

[luizirber]

someone else's code, I don't R =]