Crashes R

[jamesrgraham]

Hello,

I've installed McSearch and worked out the BABEL_LIBDIR issue, so now it can access the plug-ins.

It seems that the fatal crash occurs in this line:

std.sdf <- smiles2sdf(score.matrix[p,7])

I added some print statements to see where the crash was occurring and it has a fatal crash right after print ("inside p loop\n"), so print ("inside p loop std.sdf\n") does not get executed.

print ("inside p loop\n")
std.sdf <- smiles2sdf(score.matrix[p,7])
print ("inside p loop std.sdf\n") <-- this does not get printed out as there's a fatal error

Any ideas?

Thanks!
James

[jamesrgraham]

Here's a sample of score.matrix, if it helps:

"CSS intensity score" "matched HNL No." "std HNL No." "name" "formula" "database No." "SMILES" "InChIKey" "ion mode" "705" 0.892599234308622 1 3 "2,3-Butanediol" "C4H10O2" 1621 "OC(C)C(O)C" "OWBTYPJTUOEWEK-UHFFFAOYSA-N" "P" "1035" 0.892599234308622 1 3 "3-Methyl-2-oxovaleric acid" "C6H10O3" 2508 "O=C(O)C(=O)C(C)CC" "JVQYSWDUAOAHFM-UHFFFAOYSA-N" "N" "1094" 0.892599234308622 1 3 "beta-Cyano-alanine" "C4H6N2O2" 2617 "N#CCC(N)C(=O)O" "BXRLWGXPSRYJDZ-VKHMYHEASA-N" "N" "1202" 0.892599234308622 1 3 "Oxalacetic acid" "C4H4O5" 2903 "O=C(O)C(=O)CC(=O)O" "KHPXUQMNIQBQEV-UHFFFAOYSA-N" "N" "816" 0.577693765596009 2 6 "Ethanolamine" "C2H7NO" 1923 "OCCN" "HZAXFHJVJLSVMW-UHFFFAOYSA-N" "P" "772" 0.707089104179903 1 3 "Acetohydroxamic acid" "C2H5NO2" 1730 "ON=C(O)C" "RRUDCFGSUDOHDG-UHFFFAOYSA-N" "P"

[Philipbear]

Hi,

It looks like it's directly related to the smiles2sdf function in ChemmineR packge.

Here are some links that might be useful:
https://rdrr.io/bioc/ChemmineR/man/smiles2sdf.html
https://bioconductor.org/packages/devel/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html

You may want to save the smiles column of the data frame and pass the vector to the function to test it out.

Shipei

[flynion]

Thanks Shipei! From: Shipei Xing ***@***.***> Sent: September 1, 2023 12:14 PM To: HuanLab/McSearch ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [HuanLab/McSearch] Crashes R (Issue #2) [CAUTION: Non-UBC Email] Hi, It looks like it's directly related to the smiles2sdf function in ChemmineR packge. Here are some links that might be useful: https://rdrr.io/bioc/ChemmineR/man/smiles2sdf.html https://bioconductor.org/packages/devel/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html You may want to save the smiles column of the data frame and pass the vector to the function to test it out. Shipei — Reply to this email directly, view it on GitHub <#2 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMQU4Y6NPTEVVQN7C4SMFR3XYIXYZANCNFSM6AAAAAA4GLKWSA> . You are receiving this because you are subscribed to this thread. <https://github.com/notifications/beacon/AMQU4YZOKFMGY2FAUCDDOULXYIXYZA5CNFSM6AAAAAA4GLKWSCWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTFQUEDA.gif> Message ID: ***@***.*** ***@***.***> >

[jamesrgraham]

Hello again,

Thanks for your responses. I seem to have solved the main issue and the code runs and produces the following output before crashing again:

The score matrix has 100 rows.

Can there be an issue in my mzXML file? Sometimes, fewer output files such as this latest run:

This second run produced fewer files before the crash.

Any ideas?

[Philipbear]

Hi,

To be honest, I do not have any idea at this moment. If you feel like there might be issues related to the mzXML file, you can extract all MS2 spectra into an mgf file and load them back. R crashing is usually accompanied with some fatal function error or out-of-memory issue.

[jamesrgraham]

Thanks, Philip.

Do you have any test mzXML files that you know work that I could try for testing?

I'll try the other version, which requires the MGF format.