Welcome to tima-r Discussions!

[Adafede]

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[qfavregod]

Hi Adriano! Thank you for the amazing job you have done so far. I am facing an error when tryin to run Rscript to install.R:

Current version is the latest, no need to update.
✔ Loading metadata database ... done
✖ Creating lockfile pkg.lock [8.1s]
Error:
! error in pak subprocess
Caused by error in readRDS(dbfile):
! error reading from connection

Backtrace:

1. pak::lockfile_create()
2. pak:::remote(function(...) { …
3. err$throw(res$error)

---

Subprocess backtrace:

1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("lockfile_create_internal", asNamespace("pak"))(...)
3. prop$solve()
4. private$plan$solve(policy = private$policy)
5. pkgdepends:::pkgplan_solve(self, private, match.arg(policy))
6. self$resolve()
7. pkgdepends:::pkgplan_resolve(self, private)
8. pkgdepends:::synchronise(self$async_resolve())
9. asNamespace("pkgcache")$synchronise(...)
10. base::stop(priv$value)
11. global (function (e) …
    Execution halted

Any suggestions... Thx

[Adafede]

Hey Quentin! Thank you for the compliments. Looks like a weird error there is not much I could do to reproduce. Could you try running the command again? Maybe some process got stuck by pure unluck...disk space, internet connexion or else?

[adrien-jagora]

Hi Adriano! I've followed your advice and created a Github account for the occasion ! I had one additionnal question regarding the optional MS1-based annotation on Lotus. If I understand correctly, this happens when the score S1 equals 0 as a way to allow TimaR to do its taxonomical annotation later on. Is this MS1 dereplication based on the exact mass of the precursor ion considered or on a molecular formula previously generated ? Thanks in advance !

[Adafede]

Hi @adrien-jagora,

Nice to see you created a GitHub account!

Regarding your question, best is if you ask it on a separate thread so that people can search for it later and not in here as it might not be the best for findability.

I'll open one for you.

[adrien-jagora]

Ok, thanks !

[Y-Thom]

Dear Dr. Rutz
I started a job on TimaR with annotations obtained on sirius 6 and I get an error message.
No problem running the same job without the .zip folder which contains all the .tsv or .csv files obtained after the sirius 6 “all hits” summaries, but when I load the .zip and run it, the script stops on this error:
Warning: Error in : Error in tar_make():
file must be a length one character vector or numeric
See https://books.ropensci.org/targets/debugging.html

Attached is the R output after launching the app.
runApp().txt

Do I have a format problem with the Sirius annotation files?

Many thanks for your help,

Best regards,

runApp().txt

[Adafede]

Dear @Y-Thom,

Thank you for the detailed logs.

Could you also send the path you provided for your Sirius job? And the content of the folder? Hopefully this will help finding the issue.

Best,

Adriano

[Y-Thom]

Thank you for your fast reply !
My Sirius data summaries are located here : "C:\Users\CEVAMAP\GitHub\tima-main\data\interim\PYRAMIMONAS.zip"
And here is the content of the .zip
https://www.grosfichiers.com/Mr6N3eg5YVy

Thank you for your time and help,

Best regards,

[Adafede]

Hi again,

It looks like canopus summaries are missing from your SIRIUS results. This is highly likely the reason of your job failing with SIRIUS results.

Since TIMA is using the chemical classes for reranking, they are not optional (yet, at least). You can obtain them with the classes flag as indicated in
https://taxonomicallyinformedannotation.github.io/tima/articles/II-preparing.html#sirius

Hope this helps,

Adriano

[Y-Thom]

Hello,
Thank you for your help, it was impossible to get the canopus file with the version of sirius I was using (6.0.1) but with the new version ( 6.2.2) I no longer have this problem. Thanks a lot!