Automatic logs in the working directory create problems for docker containers

[saezlab]

Automatic logs in the working directory create problems for docker containers

[deeenes]

Hi @dpryan79,

I backported this to Bioc 3.13, OmnipathR 3.0.1 has been propagated already for Linux and OSX, hopefully it will be updated also for Windows soon: http://bioconductor.org/packages/3.13/bioc/html/OmnipathR.html

Best,

Denes

[deeenes]

You are right, now in 3.0.4 and 3.1.4 I made the options set before package loading to be preserved. These changes will be in BioC 3.13 and 3.14 hopefully soon.

[deeenes]

Hi,

That's a good point. One solution could be if you create a config file at <user_config_path>/OmnipathR/omnipathr.yml with the content:

default
  omnipath.logfile: /dev/null

Alternatively, I can add an option to disable logging, which could be set from the config file or by an environment variable. Let me know if you prefer this.

Best,

Denes

[dpryan79]

An option would probably be easiest :)

[deeenes]

Hi @dpryan79,

Since 38757b4 if you set the parameter omnipath.logfile to none , the logging to file is disabled. In the config file it looks like this:

default
  omnipath.logfile: none

Alternatively, the parameter can be set by an environment variable:

$ export OMNIPATH_LOGFILE="none"
$ R
> library(OmnipathR)
>

I hope this helps. This is currently here in our git repo, in version 3.1.2. I am wondering if there is a way to backport it to Bioc 3.13?

Best,

Denes

[dpryan79]

Awesome, thanks!

[dpryan79]

You should be able to post a bugfix update to the current bioconductor release. You'll need to bump the version to 3.0.1. Other than that I don't really know how the Bioconductor release process works.

[bersbersbers]

I am not quite sure what the use of omnipath.logfile is: it does not seem to be useful to suppress creation of the logfile, supposedly because OmnipathR overwrites that option on first load and immediately creates the log file. See here:

options(omnipath.logfile='none')

getOption('omnipath.logfile')
[1] "none"

OmnipathR:::omnipath_has_logfile()
[1] TRUE

getOption('omnipath.logfile')
NULL

I found export OMNIPATH_LOGFILE="none" very useful, but I wonder how I can suppress creation of the log file from within R.

Sys.setenv(OMNIPATH_LOGFILE = 'none')
OmnipathR:::omnipath_has_logfile()

works ;)

[bersbersbers]

Thanks, confirmed!