NA/NaN error in convert_output() for SS3 output (v3.30.24.2)

[alexjensen-NOAA]

I am trying to convert SS3 output for a previous Pacific mackerel assessment using stockplotr::convert_output, and I am seeing the following error message:
...
→ Processing NUMBERS_AT_AGE
ℹ FACTORS REMOVED: NUMBERS_AT_AGE - beg/mid
→ Processing NUMBERS_AT_LENGTH
ℹ FACTORS REMOVED: NUMBERS_AT_LENGTH - beg/mid
→ Processing SPAWN_RECRUIT
Error in 1:rownum : NA/NaN argument

Have you seen this error before, and how would you recommend I troubleshoot these types of errors? I get no warnings about improper inputs/outputs/syntax when I run and summarize this model using SS3 v3.30.24.2.

I tried to attach the corresponding Report.sso but was unable to do so based on GitHub restrictions. I can email it if useful to help reproduce the problem.

Alex

[Schiano-NOAA]

Thanks for bringing this issue to our attention! Yes, if you could email me the file, it would be very helpful in debugging. This sounds like something internal and something specific to that model configuration that is throwing the error.

After sending me the file, could you try converting the output from the r4ss::ss_output function? So follow the process to make an R object from the model output, then run that object through convert_output. That should be a viable alternative until I get the bug sorted.

[alexjensen-NOAA]

Hi Sam, Thanks for your help with this issue. I've attached the Report.sso for Pacific mackerel. And I confirmed that running the ss_output() R object through convert_output() works just fine in the interim, so thanks for that temporary fix! Best, Alex

…

On Wed, Sep 16, 2026 at 6:17 AM Sam (Schiano) Bredeck < ***@***.***> wrote: *Schiano-NOAA* left a comment (nmfs-ost/stockplotr#370) <#370 (comment)> Thanks for bringing this issue to our attention! Yes, if you could email me the file, it would be very helpful in debugging. This sounds like something internal and something specific to that model configuration that is throwing the error. After sending me the file, could you try converting the output from the r4ss::ss_output function <https://github.com/r4ss/r4ss/blob/main/R/SS_output.R>? So follow the process to make an R object from the model output, then run that object through convert_output. That should be a viable alternative until I get the bug sorted. — Reply to this email directly, view it on GitHub <#370?email_source=notifications&email_token=BIGZMSTD2J22NNW2EXWGCFL5PKHGHA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKNRZHAYDSMRTGAZ2M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#issuecomment-5698092303>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BIGZMSRB6RQ7LQUCBDZTHFD5PKHGHAVCNFSNUABFKJSXA33TNF2G64TZHM4DCNBWG4YDGMJZHNEXG43VMU5TKNBWG44TEMRTHEZKC5QC> . 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/BIGZMSSA5FPPBH4WDBA3IAL5PKHGHA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKNRZHAYDSMRTGAZ2M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/BIGZMSUS7BNFLFBO24T6ONT5PKHGHA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKNRZHAYDSMRTGAZ2M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you authored the thread.Message ID: ***@***.***>

[Schiano-NOAA]

Glad it worked! I don't think the file got attached, if you don't mind trying again 😄

[alexjensen-NOAA]

I see it attached on my end, so I wonder if GitHub is still stripping it. I added your NOAA email address in case that helps. Alex

…

On Wed, Sep 16, 2026 at 12:49 PM Sam (Schiano) Bredeck < ***@***.***> wrote: *Schiano-NOAA* left a comment (nmfs-ost/stockplotr#370) <#370 (comment)> Glad it worked! I don't think the file got attached, if you don't mind trying again 😄 — Reply to this email directly, view it on GitHub <#370?email_source=notifications&email_token=BIGZMSQRU724PEGKJC5T2UD5PLVEPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKNZQGM2TOMRSGM42M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#issuecomment-5703572239>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BIGZMSUBH6O75SCBWNIGG235PLVEPAVCNFSNUABFKJSXA33TNF2G64TZHM4DCNBWG4YDGMJZHNEXG43VMU5TKNBWG44TEMRTHEZKC5QC> . 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/BIGZMST6QDJRXL2BKHOW6U35PLVEPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKNZQGM2TOMRSGM42M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/BIGZMSXFERW2TFDOTI6EJEL5PLVEPA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKNZQGM2TOMRSGM42M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you authored the thread.Message ID: <nmfs-ost/stockplotr/issues/370/5703572239 ***@***.***>