rMAP error

[skyblue522]

Would greatly appreciate advice on next steps.

[GunzIvan28]

Hey @skyblue522 ,

Thanks for using the pipeline. For me to be able to troubleshoot what exactly went wrong, do share the markdown file "rMAP_report.Rmd" located in the "reports" directory. I will take it from there.

Ivan

[skyblue522]

Thank you Ivan for getting back to me. Is the attached document sufficient? Margaret

[skyblue522]

Hi Ivan, I sent the markdown file on Monday (from this email address but in a separate email). Did you receive it? Otherwise I am happy to send it again. Thanks, Margaret

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On Fri, Mar 25, 2022 at 9:38 PM Ivan ***@***.***> wrote: Hey @skyblue522 <https://github.com/skyblue522> , Thanks for using the pipeline. For me to be able to trouble shoot what exactly went wrong, kindly share the markdown file "rMAP_report.MD" located in the "reports" directory. I will take it from there. Ivan — Reply to this email directly, view it on GitHub <#9 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AYNFOXBGYISDR2IEFLH6NGLVBZ2CPANCNFSM5RVK42MA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[GunzIvan28]

Hi Margaret,

Thanks for the post. Sorry I might have missed the report as I don't see no attachment of the markdown file on this trail. Would you kindly re-upload the file or if you face any challenges, let me know so that I can provide you an email via which you could share it..

Another thing worth looking into is making sure you ran the configuration step using rMAP -c option. This installs all the markdown generation dependencies. It's very common to miss this out so we recommend you re-run it before proceeding with anything else. In case this was the problem, reach out and let me know so that I can advise what lines within the main program you have to de-activate in order for you not to repeat the time consuming run again and just generate your report instead.

Ivan

[skyblue522]

Hi Ivan,

I just realized that my emails from the last week have not reached you, I sincerely apologize. I tried uploading the file here on github, but it is an rMD file that is not compatible. You mentioned that you could provide me with an email to share the file, could you send me that address?

Margaret

[GunzIvan28]

Hey Margaret,

Sorry about that inconvenience. Find my email below:

[email protected]

Cheers,
Ivan

[dysci2022]

Hi Ivan,

This is a wonderful tool!

I encountered the same problem as Margaret. rMAP was unable to generate the final HTML file and reported an error: "quoting from lines 92-93 (rmap_report. RMD)"

I ran the command in the Ubuntu system. Here is the markdown file "rMAP_report.Rmd", which has also been sent to your email. Hope it helps!

Thanks!
Eric
rMAP_report.Rmd.zip

[GunzIvan28]

@eric,

Thanks for the compliment and the files. Let me review and troubleshoot what the error could be and revert.

[GunzIvan28]

@eric,

Thanks for the compliment and the files. Let me review and troubleshoot what the error could be and revert.

[skyblue522]

I ran the rMAP -t 8 -c command before the acinetobacter command, so I don't believe this is the issue. Are you able to access the attachment on this email? Thank you for your help! Margaret

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On Wed, Mar 30, 2022 at 5:12 PM Ivan ***@***.***> wrote: Hi Margaret, Thanks for the post. Sorry I might have missed the report as I don't see no attachment of the markdown file on this trail. Would you kindly re-upload the file or if you face any challenges, let me know so that I can provide you an email via which you could share it.. Another this worth looking into is making sure you ran the configuration step using rMAP -c option. This installs all the markdown generation dependencies. It's very common to miss this out so we recommend you re-run it before proceeding with anything else. In case this was the problem, reach out and let me know so that I can advise what lines within the main program you have to de-activate in order for you not to repeat the time consuming run again and just generate your report instead. Ivan — Reply to this email directly, view it on GitHub <#9 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AYNFOXAWLEYPMLVSI73XBMDVCTGVNANCNFSM5RVK42MA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[GunzIvan28]

Hi Margaret,

Thanks for reaching out. I still can't find any attachment. Confirm you sent it or give a clear description of the error so that I can see how to support