update package to work with SS3 version 3.30.24.2

[iantaylor-NOAA]

Inspired by an email from @JuanMatiasBraccini, I asked github copilot to update the package to work with current SS3 versions using the prompt informed by issues identified in the email:

make changes to this package to get it working with the current version of SS3 (version 3.30.24.2), available via r4ss::get_ss3_exe(). known issues include change in input filenames from ss.par to ss3.par and changes to the data.ss_new output file which is now output as 3 separate files as discussed in nmfs-ost/ss3-source-code#218"

I made some additional refinements on top of what copilot provided, including

• revising text,
• incremented the version number from 0.3.0 to 0.4.0 (but maybe it should be 0.3.1?)
• update SS3 executables from 3.30.18 to 3.30.24.2

The changes from copilot all look pretty good to me, but I've only looked over them very quickly.

@nathanvaughan-NOAA, let me know if you have any time or interest in reviewing these changes.

[iantaylor-NOAA]

I was able to work around an SS3 issue (nmfs-ost/ss3-source-code#764) by leaving the benchmarks on (which I don't think will do any harm) in c762193. However, I'm now seeing a problem in the integration test

devtools::test(filter = "interim")
i Testing SSMSE
Welcome to SSMSE version 0.4.0 using Stock Synthesis 3.30.24.2
v | F W  S  OK | Context
x | 2 1      2 | Integration test for interim assessment workflow [5.5s]            
------------------------------------------------------------------------------------
Warning (test-interim.R:33:3): run_SSMSE runs with interim assessment workflow
running command '"C:/github/SSMSE/inst/bin/Windows64/ss3.exe" -nohess' had status 1

Running the code from the test to create the failed model and then running the model outside of the test, I see the error:

Warning 4 Fatal Error! error on ss.par read; final value was not 999; total number parms changed  44.2094
Also see warning.sso
Exiting SS3!

I'm sure this won't be TOO hard to figure out, but I won't be able to get to it for at least a week. @nathanvaughan-NOAA, if you feel like debugging, feel free to fetch my branch and explore or just wait for me to get back to it in early July.

[iantaylor-NOAA]

When complete, this pull request should fix #232.
@JuanMatiasBraccini also said he can run the models with 3.30.21 and use the status-quo SSMSE as a work around.

[nathanvaughan-NOAA]

Thanks @iantaylor-NOAA I'll update you if I get a chance to continue debugging.

[iantaylor-NOAA]

@nathanvaughan-NOAA, I fixed a few additional problems causing test failures and the tests are now passing on my computer. Can you let me know if you have time to look over the additional changes and/or enable the github actions to run automated tests? I don't have repo permissions to run them myself.

[nathanvaughan-NOAA]

Hey @iantaylor-NOAA sorry I haven't had a chance to look through this sooner. I made a branch off main called dev-3-30-24-2 could you pull request into that branch so I can run the tests. It doesn't seem to want to let me run them on your fork. Nevermind, I was able to make a pull request from your fork and now the test are running in both pull requests anyway. I guess I fixed it somehow.

[nathanvaughan-NOAA]

Overall, it looks fine to me if everything is passing for you. I saw that you removed the implementation error values because you don't need them in the new version. Does that mean that this update is going to break compatibility with earlier SS versions?

[nathanvaughan-NOAA]

@iantaylor-NOAA for some reason the check_exe.R function is failing to find the ss3 executable in the MacOS_arm64 folder in all tests. I see that you updated the file but I have no idea why it isn't being found?

[iantaylor-NOAA]

@nathanvaughan-NOAA, good point about backwards compatibility. I didn't think about that during this work and I'm sure you're right that it would break for earlier SS3 versions. I don't think it would be too hard to add some switches based on the version number, but it would add complexity to the package. In theory someone wanting to run SSMSE for an older SS3 model could just install the v0.3.0 release instead of the new version. However, I'm not in touch with the users of SSMSE so I don't know how exactly it's being applied and what combinations of SS3 versions will need to be supported going forward.

I'll look into the failed MacOS action.

[nathanvaughan-NOAA]

No worries @iantaylor-NOAA I just wanted to confirm these would be breaking changes. In the SE we are running a lot of older assessments which is one of the reasons we are working on our own branch that is still on 3.30.19 :)

[iantaylor-NOAA]

@nathanvaughan-NOAA, looks like things are passing thanks to a fix in the executable permissions suggested by copilot

[nathanvaughan-NOAA]

Thanks for all you work on this @iantaylor-NOAA, let us know if you have any issues with the updates @JuanMatiasBraccini

[JuanMatiasBraccini]

OFFICIAL Hi guys, Thanks so much for the effort and time invested, much appreciated! Though unfortunately, still not managing to get it work. I updated ssmse() using Ian's branch and tested the cod model, which worked fine, but when try to run an absolute minimal run on my SS input files, it fails. If you had the chance, could you try running the attached? Cheers Matias Dr Matias Braccini | Principal Research Scientist Aquatic Science and Assessment Fisheries and Sustainability Department of Primary Industries and Regional Development 39 Northside Drive | Hillarys WA 6025 t +61 (0)8 9203 0211 | w dpird.wa.gov.au Adjunct Research Fellow School of Molecular and Life Sciences Curtin University From: Nathan Vaughan ***@***.***> Sent: Friday, 10 July 2026 10:01 PM To: nmfs-ost/SSMSE ***@***.***> Cc: Matias Braccini ***@***.***>; Mention ***@***.***> Subject: [EXT] - Re: [nmfs-ost/SSMSE] update package to work with SS3 version 3.30.24.2 (PR #233) CAUTION: This email originated from outside of DPIRD. Do not click links or open attachments unless you recognise the sender and know the content is safe. [https://avatars.githubusercontent.com/u/53061482?s=20&v=4]nathanvaughan-NOAA left a comment (nmfs-ost/SSMSE#233)<#233 (comment)> Thanks for all you work on this @iantaylor-NOAA<https://github.com/iantaylor-NOAA>, let us know if you have any issues with the updates @JuanMatiasBraccini<https://github.com/JuanMatiasBraccini> - Reply to this email directly, view it on GitHub<#233?email_source=notifications&email_token=AEAKRGQHUX3HCYSO3QVV4ZT5EDZIPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOJTGYYTANRZG432M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-4936106977>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEAKRGUASSXASBL66FCKIE35EDZIPAVCNFSNUABFKJSXA33TNF2G64TZHMYTSNZQGY4TQMBRHNEXG43VMU5TINRYGYZDMNRQGYY2C5QC>. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS<https://github.com/notifications/mobile/ios/AEAKRGTZUYSGWVGIBMIDCJ35EDZIPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOJTGYYTANRZG432M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android<https://github.com/notifications/mobile/android/AEAKRGVBA676WES35ME2YLL5EDZIPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOJTGYYTANRZG432M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>> [Facebook]<https://www.facebook.com/DPIRDWA> [x] <https://x.com/dpirdbroadacre> [Linkedin] <https://www.linkedin.com/company/dpirdwa> [Instagram] <https://www.instagram.com/dpirdwa/> [Dept of Primary Industries and Regional Development] [Protect, Grow, Innovate] [Artwork: "Kangaroos going to the Waterhole" by Willarra Barker.] DPIRD acknowledges the Traditional Custodians of Country, the Aboriginal people of the many lands that we work on and their language groups throughout Western Australia and recognise their continuing connection to the land and waters. We respect their continuing culture and the contribution they make to the life of our regions and we pay our respects to their Elders past, present and emerging. Artwork: "Kangaroos going to the Waterhole" by Willarra Barker. DISCLAIMER: The information contained in this email (including attachments) is intended only for the use of the person(s) to whom it is addressed as it may be confidential and contain legally privileged information. If you are not the intended recipient you are hereby notified that any perusal, use, distribution, copying or disclosure is strictly prohibited. If you have received this email in error, please immediately advise us by return email and delete the email document. This email and any attachments to it are also subject to copyright and any unauthorised reproduction, adaptation or transmission is prohibited. This notice should not be removed.

[iantaylor-NOAA]

@JuanMatiasBraccini, sorry to hear that it didn't work and for the slow reply. I'm just back from a week on leave and it looks like the attachment didn't go through. You could email files to ian.taylor@noaa.gov or navigate to the github issue (#233) and drag and drop files into a comment (zip is allowed, but not .ss extensions, although they can be renamed to .txt).

[iantaylor-NOAA]

@JuanMatiasBraccini, cancel that previous message. I received the attachments by your original email since it was sent to me in addition to github. I'm not sure how quickly I'll be able to work on this but hopefully in the next few days.

[JuanMatiasBraccini]

OFFICIAL That'll be awesome, thanks heaps Ian! Cheers Matias Dr Matias Braccini | Principal Research Scientist Aquatic Science and Assessment Fisheries and Sustainability Department of Primary Industries and Regional Development 39 Northside Drive | Hillarys WA 6025 t +61 (0)8 9203 0211 | w dpird.wa.gov.au Adjunct Research Fellow School of Molecular and Life Sciences Curtin University From: Ian Taylor ***@***.***> Sent: Tuesday, 21 July 2026 2:33 AM To: nmfs-ost/SSMSE ***@***.***> Cc: Matias Braccini ***@***.***>; Mention ***@***.***> Subject: [EXT] - Re: [nmfs-ost/SSMSE] update package to work with SS3 version 3.30.24.2 (PR #233) CAUTION: This email originated from outside of DPIRD. Do not click links or open attachments unless you recognise the sender and know the content is safe. [https://avatars.githubusercontent.com/u/4992918?s=20&v=4]iantaylor-NOAA left a comment (nmfs-ost/SSMSE#233)<#233 (comment)> @JuanMatiasBraccini<https://github.com/JuanMatiasBraccini>, cancel that previous message. I received the attachments by your original email since it was sent to me in addition to github. I'm not sure how quickly I'll be able to work on this but hopefully in the next few days. - Reply to this email directly, view it on GitHub<#233?email_source=notifications&email_token=AEAKRGRRKEAMWKS474DHDGL5FZQWLA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMBSGU3TSMJTGYZKM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5025791362>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEAKRGWIKS5S2T23NJLMFW35FZQWLAVCNFSNUABFKJSXA33TNF2G64TZHMYTSNZQGY4TQMBRHNEXG43VMU5TINRYGYZDMNRQGYY2C5QC>. Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS<https://github.com/notifications/mobile/ios/AEAKRGSRFBXSF2RE4DD77NL5FZQWLA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMBSGU3TSMJTGYZKM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android<https://github.com/notifications/mobile/android/AEAKRGS5PV2AKBJWFIRKU635FZQWLA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMBSGU3TSMJTGYZKM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>> [Facebook]<https://www.facebook.com/DPIRDWA> [x] <https://x.com/dpirdbroadacre> [Linkedin] <https://www.linkedin.com/company/dpirdwa> [Instagram] <https://www.instagram.com/dpirdwa/> [Dept of Primary Industries and Regional Development] [Protect, Grow, Innovate] [Artwork: "Kangaroos going to the Waterhole" by Willarra Barker.] DPIRD acknowledges the Traditional Custodians of Country, the Aboriginal people of the many lands that we work on and their language groups throughout Western Australia and recognise their continuing connection to the land and waters. We respect their continuing culture and the contribution they make to the life of our regions and we pay our respects to their Elders past, present and emerging. Artwork: "Kangaroos going to the Waterhole" by Willarra Barker. DISCLAIMER: The information contained in this email (including attachments) is intended only for the use of the person(s) to whom it is addressed as it may be confidential and contain legally privileged information. If you are not the intended recipient you are hereby notified that any perusal, use, distribution, copying or disclosure is strictly prohibited. If you have received this email in error, please immediately advise us by return email and delete the email document. This email and any attachments to it are also subject to copyright and any unauthorised reproduction, adaptation or transmission is prohibited. This notice should not be removed.