Cannot open file in xcms adjustRtime (retcor)


I have a new issue with the tool xcms adjustRtime (retcor). When I try to run it, it says that an error occured:

“Error in file(filename, “r”, encoding = encoding) :
cannot open the connection
Calls: source_local → source → file
In addition: Warning message:
In file(filename, “r”, encoding = encoding) :
cannot open file ‘/jetstream2/scratch/main/jobs/56785767/tool_files/lib.r’: No such file or directory
Execution halted”

I don’t undertsand which file cannot be found. I hope you can help me.

Best regards.

Hi @raynaudb

I’m not a member of the team so cannot really help you troubleshoot the specific issue, but generally, with clear errors like this one, it’s often better to create a bug report directly from within Galaxy using the little bug icon that you should see under the failed dataset in your history.
Galaxy’s bug report system will make sure that all relevant details about your user account and job will be forwarded to the team behind the server, which can save a lot of time compared to gathering these details from you via the forum or private messages.

Thank you very much @wm75 for your reply. I’m currently following your advice !



Hi @raynaudb

I didn’t find your bug report sent in from the server … so, if you still need help, would you please send the bug report in again? Include a link to this forum post in the comments section please if you can. I’ll look for it again once you confirm here it has been sent. Thanks!

Hi @jennaj,

Thank you a lot for your reply. I checked all questions concerning metabolomics workflow and I saw someone said that all tools were available and operational on I reloaded all my data and everything worked. I’m sorry for taking your time and i deeply thank you.

Best regards