NP Run cannot find files; execution halted?

[tuscanyguy]

I finally got PMetric to run; however I was halted with the following error message from the R-script:

Windows cannot find
'C:\Users\Robert\OneDrive\Documents\NPAG\best\1\1\outputs\NPAGreport.html'. Make sure you typed the name correctly, and then try again.**
I've gone over the naming carefully, but I don't recognize any issue. I may have the order of naming of the various scripts below within R in error?
Can someone have a look at this?
Best regards,
Rob A.

library(Pmetrics)
OS <- switch(.Platform$OS.type,unix=1,windows=2)
wd <- c("c:best")
PMtree(project="best", folder=getwd())
setwd("best”)
#Run 1 – k01,k10,v
NPrun(data="apixd.csv", cycles=1000, model="apixpo.txt")
PMload(1)

[mhovd]

Hi Robert!

This message means that the report file was not generated, usually due to a previous error during the run.
Did you see any other errors or messages during the run?

[tuscanyguy]

Thank you for your reply Marcus! See attached .jpg outputs from the error report.

Rob A.
[if this doesn't come thru; is there an email address I can send this report to?]

[mhovd]

Thank you for the logs!

In the first picture, you can see the error gfortran is not recognized....
This indicates that you either do not have gfortran installed, or that it is not in your environmental variables (PATH).

Have you installed Rtools ? It is available to install from this location: https://cran.r-project.org/bin/windows/Rtools/
Let me know, and I can provide you with instructions to add gfortran to your PATH after installation, if it is not done automatically.

[tuscanyguy]

Thank you Marcus!
Will review tonight and get back to you tomorrow.
Rob A.

[tuscanyguy]

Okay Marcus I'll install Rtools from that location tonight. Can you provide instructions on how to add gfortran to my PATH after installation?
Rob

[mnneely]

Hi Rob, looks like gfortran isn’t properly installed. There’s a line in your first picture “gfortran is not a recognized as an internal or external command…” that indicates this.

[tuscanyguy]

Thank you Michael, I’ll review and get back tomorrow. Rob A. From: Michael Neely ***@***.***> Sent: Monday, August 18, 2025 8:20 AM To: LAPKB/Pmetrics ***@***.***> Cc: Rob Ariano ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [LAPKB/Pmetrics] NP Run cannot find files; execution halted? (Discussion #273) Hi Rob, looks like gfortran isn’t properly installed. There’s a line in your first picture “gfortran is not a recognized as an internal or external command…” that indicates this. — Reply to this email directly, view it on GitHub<#273 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXIW2S36FKAOQSWUUGE4SYT3OHHHDAVCNFSM6AAAAACEDL2DXKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJUGA4DKMQ>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>> Disclaimer : This email (including any attachments or enclosed documents) is intended for the addressee(s) only and may contain privileged, proprietary or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this email in error, please notify the sender immediately, return the original (if applicable) and delete the email. Avis : Le présent courriel (y compris toute pièce jointe) est destiné à la personne ou aux personnes à qui il est adressé, et peut contenir des renseignements confidentiels, privés ou protégés par un privilège juridique. Toute utilisation, divulgation, distribution, copie ou diffusion non autorisée est strictement défendue. Si vous avez reçu le présent courriel par erreur, veuillez en informer immédiatement l’expéditeur, retourner l’original (le cas échéant) et supprimer ce courriel.

[tuscanyguy]

Hi Markus, I’ve installed Rtools from this location: https://cran.r-project.org/bin/windows/Rtools/ Can I have the instructions to add gfortran to my PATH. Sincerely, Rob A. From: Markus Hovd ***@***.***> Sent: Monday, August 18, 2025 8:17 AM To: LAPKB/Pmetrics ***@***.***> Cc: Rob Ariano ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [LAPKB/Pmetrics] NP Run cannot find files; execution halted? (Discussion #273) Thank you for the logs! In the first picture, you can see the error gfortran is not recognized.... This indicates that you either do not have gfortran installed, or that it is not in your environmental variables (PATH). Have you installed Rtools ? It is available to install from this location: https://cran.r-project.org/bin/windows/Rtools/ Let me know, and I can provide you with instructions to add gfortran to your PATH after installation, if it is not done automatically. — Reply to this email directly, view it on GitHub<#273 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXIW2S4EZ5XOAGAKJA3ED5T3OHG5LAVCNFSM6AAAAACEDL2DXKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJUGA4DGMI>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>> Disclaimer : This email (including any attachments or enclosed documents) is intended for the addressee(s) only and may contain privileged, proprietary or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this email in error, please notify the sender immediately, return the original (if applicable) and delete the email. Avis : Le présent courriel (y compris toute pièce jointe) est destiné à la personne ou aux personnes à qui il est adressé, et peut contenir des renseignements confidentiels, privés ou protégés par un privilège juridique. Toute utilisation, divulgation, distribution, copie ou diffusion non autorisée est strictement défendue. Si vous avez reçu le présent courriel par erreur, veuillez en informer immédiatement l’expéditeur, retourner l’original (le cas échéant) et supprimer ce courriel.

[mhovd]

Great! I was able to find this guide with images: https://www.hanss.info/sebastian/post/rtools-path/

You want to make sure that you have e.g. C:\Program Files\Rtools42\mingw64\bin in the PATH. Be sure to change the location to where you actually installed Rtools.

To check that you have done everything correctly, open a terminal window and type gfortran.

[tuscanyguy]

Thank you Markus! I'll start working on that. Rob A.

…

________________________________ From: Markus Hovd ***@***.*** Sent: Wednesday, August 20, 2025 12:47 AM To: LAPKB/Pmetrics Cc: Rob Ariano; Author Subject: [EXTERNAL] Re: [LAPKB/Pmetrics] NP Run cannot find files; execution halted? (Discussion #273) Great! I was able to find this guide with images: https://www.hanss.info/sebastian/post/rtools-path/ You want to make sure that you have e.g. C:\Program Files\Rtools42\mingw64\bin in the PATH. Be sure to change the location to where you actually installed Rtools. To check that you have done everything correctly, open a terminal window and type gfortran. — Reply to this email directly, view it on GitHub<#273 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXIW2S5SGQIPW44TYPRYMMT3OQDVXAVCNFSM6AAAAACEDL2DXKVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMJWGA3DEMA>. You are receiving this because you authored the thread.Message ID: ***@***.***> Disclaimer : This email (including any attachments or enclosed documents) is intended for the addressee(s) only and may contain privileged, proprietary or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this email in error, please notify the sender immediately, return the original (if applicable) and delete the email. Avis : Le présent courriel (y compris toute pièce jointe) est destiné à la personne ou aux personnes à qui il est adressé, et peut contenir des renseignements confidentiels, privés ou protégés par un privilège juridique. Toute utilisation, divulgation, distribution, copie ou diffusion non autorisée est strictement défendue. Si vous avez reçu le présent courriel par erreur, veuillez en informer immédiatement l’expéditeur, retourner l’original (le cas échéant) et supprimer ce courriel.

[tuscanyguy]

I've tried to make those changes; however gfortran was still not present.
Can you have a look at my screenshots for following those guided images for changing PATH statements?

Steps taken for Rtools.docx

[mhovd]

Thank you for the detailed reply!

Can you confirm that you are able to navigate to the folder C:\Program Files\Rtools42\mingw64\bin, and see gfortran.exe there?
Or is your folder actually C:\Program Files\Rtools45\mingw64\bin? Notice the Rtools45 instead of Rtools42.

If you are not able to see any of those, please send me an e-mail at markus.hovd@farmasi.uio.no with some time slots you would be available for a video call, and I can guide you through it :)

[tuscanyguy]

thank you so much! I'll quickly review tonight and get back to you.
Rob