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coancestry crashing R on Windows #12

Open neellab-umd opened 1 year ago

neellab-umd commented 1 year ago

Hi Tim -

I just downloaded related from your repository and installed it according to the tutorial instructions. I have used related for years with no issue, but needed to get it again for the latest version of R. I am using coancestry() on a data set with 321 observations and 10 loci that has worked in the past. R is now terminating with the dreaded time bomb aborted session message but is giving no other information. I tested it with your GenotypeData and it is also crashing on that. Both run for quite a awhile before quitting. I have checked the memory while it is running and I do not seem to be close to running out.

My session info is R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

And I am running R within RStudio 2022.12.0 Build 353.

I know you maintain this out of the goodness of your heart and I very much appreciate it. related is the only package I can find that calculates relatedness and I depend on it!

Hoping there is an easy fix!

Maile

timothyfrasier commented 1 year ago

Hi Maile:

Oh no, I'm sorry to hear that. Admittedly, I have not updated R in a while, so I have not seen this issue. I will take a look at it in the next week or so and see if I can figure out what is going on.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Tuesday, January 3, 2023 5:29 PM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim -

I just downloaded related from your repository and installed it according to the tutorial instructions. I have used related for years with no issue, but needed to get it again for the latest version of R. I am using coancestry() on a data set with 321 observations and 10 loci that has worked in the past. R is now terminating with the dreaded time bomb aborted session message but is giving no other information. I tested it with your GenotypeData and it is also crashing on that. Both run for quite a awhile before quitting. I have checked the memory while it is running and I do not seem to be close to running out.

My session info is R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

And I am running R within RStudio 2022.12.0 Build 353.

I know you maintain this out of the goodness of your heart and I very much appreciate it. related is the only package I can find that calculates relatedness and I depend on it!

Hoping there is an easy fix!

Maile

— Reply to this email directly, view it on GitHubhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftimothyfrasier%2Frelated%2Fissues%2F12&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Ce091bc8789c2465dd67e08daedd1a49a%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638083781909234406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TlqfMx%2Fzho%2BH7yDDLWz4Dtc647QGVTLsLYaHz4Yj%2BuA%3D&reserved=0, or unsubscribehttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAA3NYWK4TDWXQRPRG62JDATWQSK4ZANCNFSM6AAAAAATQDMGHQ&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Ce091bc8789c2465dd67e08daedd1a49a%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638083781909234406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HFObjcd8uWTkByyz8fadt9flAmFRYeyTdTGweJ%2FzIwM%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

neellab-umd commented 1 year ago

Thank you so much! Given the timing of the crash, my sense is R is unhappy with something is being written out to my computer (which you note is why you don't have related on CRAN). Fingers crossed it is an easy fix. I tried going back to an earlier R version but the dependency on ggplot2 has so far prevented me from being successful at that.

Thanks Tim!

neellab-umd commented 1 year ago

Hi Tim!

Have you had a chance to look at related? I checked github and don't see any recent updates. Also, I tested the existing package with the new R version that was just released last month in the hopes that the gremlins were eliminated, but no joy.

Thanks in advance,

Maile

On Wed, Jan 4, 2023 at 11:15 AM timothyfrasier @.***> wrote:

Hi Maile:

Oh no, I'm sorry to hear that. Admittedly, I have not updated R in a while, so I have not seen this issue. I will take a look at it in the next week or so and see if I can figure out what is going on.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Tuesday, January 3, 2023 5:29 PM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] coancestry crashing R on Windows (Issue

12)

Hi Tim -

I just downloaded related from your repository and installed it according to the tutorial instructions. I have used related for years with no issue, but needed to get it again for the latest version of R. I am using coancestry() on a data set with 321 observations and 10 loci that has worked in the past. R is now terminating with the dreaded time bomb aborted session message but is giving no other information. I tested it with your GenotypeData and it is also crashing on that. Both run for quite a awhile before quitting. I have checked the memory while it is running and I do not seem to be close to running out.

My session info is R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

And I am running R within RStudio 2022.12.0 Build 353.

I know you maintain this out of the goodness of your heart and I very much appreciate it. related is the only package I can find that calculates relatedness and I depend on it!

Hoping there is an easy fix!

Maile

— Reply to this email directly, view it on GitHub< https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftimothyfrasier%2Frelated%2Fissues%2F12&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Ce091bc8789c2465dd67e08daedd1a49a%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638083781909234406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TlqfMx%2Fzho%2BH7yDDLWz4Dtc647QGVTLsLYaHz4Yj%2BuA%3D&reserved=0>, or unsubscribe< https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAA3NYWK4TDWXQRPRG62JDATWQSK4ZANCNFSM6AAAAAATQDMGHQ&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Ce091bc8789c2465dd67e08daedd1a49a%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638083781909234406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HFObjcd8uWTkByyz8fadt9flAmFRYeyTdTGweJ%2FzIwM%3D&reserved=0

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timothyfrasier commented 1 year ago

Hi Maile:

I am having trouble finding a Windows computer that I can use for testing. I have found one now, but it has taken a while. I should be able to have it tested by the end of the week.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Monday, April 17, 2023 11:31 AM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim!

Have you had a chance to look at related? I checked github and don't see any recent updates. Also, I tested the existing package with the new R version that was just released last month in the hopes that the gremlins were eliminated, but no joy.

Thanks in advance,

Maile

On Wed, Jan 4, 2023 at 11:15 AM timothyfrasier @.***> wrote:

Hi Maile:

Oh no, I'm sorry to hear that. Admittedly, I have not updated R in a while, so I have not seen this issue. I will take a look at it in the next week or so and see if I can figure out what is going on.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Tuesday, January 3, 2023 5:29 PM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] coancestry crashing R on Windows (Issue

12)

Hi Tim -

I just downloaded related from your repository and installed it according to the tutorial instructions. I have used related for years with no issue, but needed to get it again for the latest version of R. I am using coancestry() on a data set with 321 observations and 10 loci that has worked in the past. R is now terminating with the dreaded time bomb aborted session message but is giving no other information. I tested it with your GenotypeData and it is also crashing on that. Both run for quite a awhile before quitting. I have checked the memory while it is running and I do not seem to be close to running out.

My session info is R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

And I am running R within RStudio 2022.12.0 Build 353.

I know you maintain this out of the goodness of your heart and I very much appreciate it. related is the only package I can find that calculates relatedness and I depend on it!

Hoping there is an easy fix!

Maile

— Reply to this email directly, view it on GitHub< https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftimothyfrasier%2Frelated%2Fissues%2F12&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Ce091bc8789c2465dd67e08daedd1a49a%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638083781909234406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TlqfMx%2Fzho%2BH7yDDLWz4Dtc647QGVTLsLYaHz4Yj%2BuA%3D&reserved=0>, or unsubscribe< https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAA3NYWK4TDWXQRPRG62JDATWQSK4ZANCNFSM6AAAAAATQDMGHQ&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Ce091bc8789c2465dd67e08daedd1a49a%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638083781909234406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HFObjcd8uWTkByyz8fadt9flAmFRYeyTdTGweJ%2FzIwM%3D&reserved=0

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neellab-umd commented 1 year ago

Thank you so much! If there is anything I can do to help please let me know.

Maile

On Tue, Apr 18, 2023 at 10:21 AM timothyfrasier @.***> wrote:

Hi Maile:

I am having trouble finding a Windows computer that I can use for testing. I have found one now, but it has taken a while. I should be able to have it tested by the end of the week.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Monday, April 17, 2023 11:31 AM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim!

Have you had a chance to look at related? I checked github and don't see any recent updates. Also, I tested the existing package with the new R version that was just released last month in the hopes that the gremlins were eliminated, but no joy.

Thanks in advance,

Maile

On Wed, Jan 4, 2023 at 11:15 AM timothyfrasier @.***> wrote:

Hi Maile:

Oh no, I'm sorry to hear that. Admittedly, I have not updated R in a while, so I have not seen this issue. I will take a look at it in the next week or so and see if I can figure out what is going on.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Tuesday, January 3, 2023 5:29 PM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] coancestry crashing R on Windows (Issue

12)

Hi Tim -

I just downloaded related from your repository and installed it according to the tutorial instructions. I have used related for years with no issue, but needed to get it again for the latest version of R. I am using coancestry() on a data set with 321 observations and 10 loci that has worked in the past. R is now terminating with the dreaded time bomb aborted session message but is giving no other information. I tested it with your GenotypeData and it is also crashing on that. Both run for quite a awhile before quitting. I have checked the memory while it is running and I do not seem to be close to running out.

My session info is R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

And I am running R within RStudio 2022.12.0 Build 353.

I know you maintain this out of the goodness of your heart and I very much appreciate it. related is the only package I can find that calculates relatedness and I depend on it!

Hoping there is an easy fix!

Maile

— Reply to this email directly, view it on GitHub<

https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftimothyfrasier%2Frelated%2Fissues%2F12&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Ce091bc8789c2465dd67e08daedd1a49a%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638083781909234406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TlqfMx%2Fzho%2BH7yDDLWz4Dtc647QGVTLsLYaHz4Yj%2BuA%3D&reserved=0>,

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neellab-umd commented 1 year ago

Hi There Tim -

I am checking in again to see if there is any progress on getting related to work with the current version of R.

Thanks!

Maile

On Tue, Apr 18, 2023 at 10:42 AM Maile @.***> wrote:

Thank you so much! If there is anything I can do to help please let me know.

Maile

On Tue, Apr 18, 2023 at 10:21 AM timothyfrasier @.***> wrote:

Hi Maile:

I am having trouble finding a Windows computer that I can use for testing. I have found one now, but it has taken a while. I should be able to have it tested by the end of the week.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Monday, April 17, 2023 11:31 AM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim!

Have you had a chance to look at related? I checked github and don't see any recent updates. Also, I tested the existing package with the new R version that was just released last month in the hopes that the gremlins were eliminated, but no joy.

Thanks in advance,

Maile

On Wed, Jan 4, 2023 at 11:15 AM timothyfrasier @.***> wrote:

Hi Maile:

Oh no, I'm sorry to hear that. Admittedly, I have not updated R in a while, so I have not seen this issue. I will take a look at it in the next week or so and see if I can figure out what is going on.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Tuesday, January 3, 2023 5:29 PM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] coancestry crashing R on Windows (Issue

12)

Hi Tim -

I just downloaded related from your repository and installed it according to the tutorial instructions. I have used related for years with no issue, but needed to get it again for the latest version of R. I am using coancestry() on a data set with 321 observations and 10 loci that has worked in the past. R is now terminating with the dreaded time bomb aborted session message but is giving no other information. I tested it with your GenotypeData and it is also crashing on that. Both run for quite a awhile before quitting. I have checked the memory while it is running and I do not seem to be close to running out.

My session info is R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

And I am running R within RStudio 2022.12.0 Build 353.

I know you maintain this out of the goodness of your heart and I very much appreciate it. related is the only package I can find that calculates relatedness and I depend on it!

Hoping there is an easy fix!

Maile

— Reply to this email directly, view it on GitHub<

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timothyfrasier commented 1 year ago

Hi Maile:

No, I'm afraid not. My summer is very busy, and I will likely not have time to work on it in the near future.

However, I am working on getting someone to work on a complete re-write of related in the fall, to deal with the existing issues, as well as update it for allowing it to work with large SNP data sets. Of course, another goal will be to make it more "forward-thinking", meaning more dynamic as R and analysis needs change.

I know this doesn't help you now, but updating this package, and making it less "touchy" is on my priority list, and we will hopefully get started on this in the fall.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Monday, June 5, 2023 11:17 AM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi There Tim -

I am checking in again to see if there is any progress on getting related to work with the current version of R.

Thanks!

Maile

On Tue, Apr 18, 2023 at 10:42 AM Maile @.***> wrote:

Thank you so much! If there is anything I can do to help please let me know.

Maile

On Tue, Apr 18, 2023 at 10:21 AM timothyfrasier @.***> wrote:

Hi Maile:

I am having trouble finding a Windows computer that I can use for testing. I have found one now, but it has taken a while. I should be able to have it tested by the end of the week.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Monday, April 17, 2023 11:31 AM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim!

Have you had a chance to look at related? I checked github and don't see any recent updates. Also, I tested the existing package with the new R version that was just released last month in the hopes that the gremlins were eliminated, but no joy.

Thanks in advance,

Maile

On Wed, Jan 4, 2023 at 11:15 AM timothyfrasier @.***> wrote:

Hi Maile:

Oh no, I'm sorry to hear that. Admittedly, I have not updated R in a while, so I have not seen this issue. I will take a look at it in the next week or so and see if I can figure out what is going on.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Tuesday, January 3, 2023 5:29 PM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] coancestry crashing R on Windows (Issue

12)

Hi Tim -

I just downloaded related from your repository and installed it according to the tutorial instructions. I have used related for years with no issue, but needed to get it again for the latest version of R. I am using coancestry() on a data set with 321 observations and 10 loci that has worked in the past. R is now terminating with the dreaded time bomb aborted session message but is giving no other information. I tested it with your GenotypeData and it is also crashing on that. Both run for quite a awhile before quitting. I have checked the memory while it is running and I do not seem to be close to running out.

My session info is R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

And I am running R within RStudio 2022.12.0 Build 353.

I know you maintain this out of the goodness of your heart and I very much appreciate it. related is the only package I can find that calculates relatedness and I depend on it!

Hoping there is an easy fix!

Maile

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neellab-umd commented 1 month ago

Hi Tim -

I am checking in to see if there has been any progress getting related to work with R 4.0 and beyond. I see that the note on the repository says that related should now work on R 4.2 and beyond, but I am still having the same crashing issue at the end of the analysis.

Best,

Maile

timothyfrasier commented 1 month ago

Hi Maile:

I am using it on R 4.4.0 (on a linux OS), and it is working fine. Can you please provide more information. What operating system are you using? When is it crashing (after running what function)?

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Monday, June 17, 2024 11:28 AM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim -

I am checking in to see if there has been any progress getting related to work with R 4.0 and beyond. I see that the note on the repository says that related should now work on R 4.2 and beyond, but I am still having the same crashing issue at the end of the analysis.

Best,

Maile

— Reply to this email directly, view it on GitHubhttps://github.com/timothyfrasier/related/issues/12#issuecomment-2173573977, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA3NYWLTNROFJDHMJA6WUGLZH3W7RAVCNFSM6AAAAABJOEANBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZTGU3TGOJXG4. You are receiving this because you commented.Message ID: @.***>

neellab-umd commented 1 month ago

Hi Tim -

I am running under: Windows 11 x64 (build 22631) on one machine and Windows 10 on another, with the same results

I get the results with R version 4.3.3 (2024-02-29 ucrt), Platform: x86_64-w64-mingw32/x64 and R version 4.4.0 (2024-04-24 ucrt), Platform: x86_64-w64-mingw32/x64

My data set has 941 individuals and 10 loci. These functions have worked perfectly with this data set in the past.

Now when I use the coancestry() or grouprel() functions, the process will run but after ~2 hours just when it seems like it should be writing out results, the session aborts. The message says that R encountered a fatal error and the session was terminated.

The coancestry and grouprel functions also yield aborted R sessions when I use the GenotypeData.txt file you provide with the package. So I do not think it is an issue with my data set.

I am submitting to a journal that requires all r scripts to be submitted and I am concerned that the analysis cannot be confirmed as the script no longer works. I really do not want to cut out these results because they add a lot to the manuscript.

Thanks for any help you can provide.

Best,

Maile

timothyfrasier commented 1 month ago

Hi Maile:

I just did a clean install of related on a Windows computer. The configuration was:

Windows 10 R version 4.4.1

I ran the functions that you mentioned on the example file, and everything ran fine.

In hindsight, it seems like it must have to do with the available RAM on your computer. The fact that you could successfully install related on your computer, and that it began running the functions, means that everything is working fine. The fact that you are getting errors when it should be writing files suggests a memory problem.

Do you have a larger computer that you could run your analyses on?

Sincerely, Tim Frasier

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Wednesday, June 19, 2024 3:44 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim -

I am running under: Windows 11 x64 (build 22631) on one machine and Windows 10 on another, with the same results

I get the results with R version 4.3.3 (2024-02-29 ucrt), Platform: x86_64-w64-mingw32/x64 and R version 4.4.0 (2024-04-24 ucrt), Platform: x86_64-w64-mingw32/x64

My data set has 941 individuals and 10 loci. These functions have worked perfectly with this data set in the past.

Now when I use the coancestry() or grouprel() functions, the process will run but after ~2 hours just when it seems like it should be writing out results, the session aborts. The message says that R encountered a fatal error and the session was terminated.

The coancestry and grouprel functions also yield aborted R sessions when I use the GenotypeData.txt file you provide with the package. So I do not think it is an issue with my data set.

I am submitting to a journal that requires all r scripts to be submitted and I am concerned that the analysis cannot be confirmed as the script no longer works. I really do not want to cut out these results because they add a lot to the manuscript.

Thanks for any help you can provide.

Best,

Maile

— Reply to this email directly, view it on GitHubhttps://github.com/timothyfrasier/related/issues/12#issuecomment-2179305811, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA3NYWJBN3A5DNINVCYFGMLZIHGSBAVCNFSM6AAAAABJOEANBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZZGMYDKOBRGE. You are receiving this because you commented.Message ID: @.***>

neellab-umd commented 1 month ago

Where should I be getting related - from sourceforge or github? Are they the same? I think I have tried both of these sources and am not sure which one I have installed now. I can try uninstalling and reinstalling from the source you suggest.

I have been having the problem over two years with multiple installations of related and any version of R after 4.0. Today I changed to R4.4.1 and have the same issues. Up until R 4.0 I was able to use coancestry() and grouprel() on this same dataset with no issues.

I get the fatal error on both my computers. My Windows 11 machine has 32 GB of RAM. My windows 10 machine has 128GB of RAM. Neither are anywhere near capacity while running coancestry (21% and 40% total memory used on each machine, respectively as per task manager). My computer I had at the time I could run these functions had less RAM than the two computers I have now.

I even pared your GenotypeData.txt dataset down to the first 45 individuals and it crashes immediately. So I do not think it is a memory issue.

I can't think of why it would be working on your windows machine and not mine.

The one nagging suspicion I have is that the last line in your data file is a blank line. The difference between the end of line character between windows and Mac/Linux caused me no end of headaches going between operating systems. But that doesn't seem like it would be the issue if it works on your windows machine.

timothyfrasier commented 1 month ago

Hi:

That behaviour is very strange. If the installation did not cause errors, then it should run without any problems - particularly with the example data set.

You should download the source code and the example data file directly from github (herehttps://github.com/timothyfrasier/related). To install it properly on Windows, you also need to install RTools (herehttps://cran.r-project.org/bin/windows/Rtools/). I got an error when I tried the latest tool of RTools (4.4), but it worked fine when I used 4.3. So I would recommend installing 4.3.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Monday, June 24, 2024 4:02 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Where should I be getting related - from sourceforge or github? Are they the same? I think I have tried both of these sources and am not sure which one I have installed now. I can try uninstalling and reinstalling from the source you suggest.

I have been having the problem over two years with multiple installations of related and any version of R after 4.0. Today I changed to R4.4.1 and have the same issues. Up until R 4.0 I was able to use coancestry() and grouprel() on this same dataset with no issues.

I get the fatal error on both my computers. My Windows 11 machine has 32 GB of RAM. My windows 10 machine has 128GB of RAM. Neither are anywhere near capacity while running coancestry (21% and 40% total memory used on each machine, respectively as per task manager). My computer I had at the time I could run these functions had less RAM than the two computers I have now.

I even pared your GenotypeData.txt dataset down to the first 45 individuals and it crashes immediately. So I do not think it is a memory issue.

I can't think of why it would be working on your windows machine and not mine.

The one nagging suspicion I have is that the last line in your data file is a blank line. The difference between the end of line character between windows and Mac/Linux caused me no end of headaches going between operating systems. But that doesn't seem like it would be the issue if it works on your windows machine.

— Reply to this email directly, view it on GitHubhttps://github.com/timothyfrasier/related/issues/12#issuecomment-2187218870, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA3NYWL2MR7OG3ZJ3PNSVHLZJBUNTAVCNFSM6AAAAABJOEANBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBXGIYTQOBXGA. You are receiving this because you commented.Message ID: @.***>

neellab-umd commented 1 month ago

Hi Tim -

Just to confirm - I downloaded the related_1.0.tar.gz that indicates it is for R 3.5 - that is the only install file I see at https://github.com/timothyfrasier/related.

I uninstalled related using remove.packages()

I had both Rtools 4.3 and 4.4 installed, but at your suggestion I uninstalled 4.4 thinking that would force R to use Rtools 4.3. But that just caused the compilation of related to exit with non-zero status. I reinstalled Rtools4.4 and installed related_1.0.tar.gz through r studio using the local file.

I get these messages and a normal exit - I don't see any errors - perhaps you can see something that I don't.

Installing package into ‘C:/Users/mneel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified)

library(related) indicates all is well

library(related) Loading required package: tools Loading required package: ggplot2

But loading and running the code in the tutorial for you test data set still crashes R with a fatal error.

timothyfrasier commented 1 month ago

Hi:

This is so strange. I wonder if having a Zoom call next week (or sometime soon) would be a good idea. That way I can see exactly what you are typing, what messages are coming up, and so on.

How does that sound to you? What day/times would you be available? What time zone are you in (I'm in Atlantic (AST))?

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Wednesday, June 26, 2024 6:04 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim -

Just to confirm - I downloaded the related_1.0.tar.gz that indicates it is for R 3.5 - that is the only install file I see at https://github.com/timothyfrasier/related.

I uninstalled related using remove.packages()

I had both Rtools 4.3 and 4.4 installed, but at your suggestion I uninstalled 4.4 thinking that would force R to use Rtools 4.3. But that just caused the compilation of related to exit with non-zero status. I reinstalled Rtools4.4 and installed related_1.0.tar.gz through r studio using the local file.

I get these messages and a normal exit - I don't see any errors - perhaps you can see something that I don't.

Installing package into ‘C:/Users/mneel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified)

library(related) indicates all is well

library(related) Loading required package: tools Loading required package: ggplot2

But loading and running the code in the tutorial for you test data set still crashes R with a fatal error.

— Reply to this email directly, view it on GitHubhttps://github.com/timothyfrasier/related/issues/12#issuecomment-2192624222, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA3NYWMCAAYQINS4AWAGAZDZJMUFVAVCNFSM6AAAAABJOEANBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJSGYZDIMRSGI. You are receiving this because you commented.Message ID: @.***>

neellab-umd commented 1 month ago

That would be WONDERFUL!!!!! I really really appreciate it. I am available today or anytime next week except Monday morning.

On Fri, Jun 28, 2024 at 11:51 AM timothyfrasier @.***> wrote:

Hi:

This is so strange. I wonder if having a Zoom call next week (or sometime soon) would be a good idea. That way I can see exactly what you are typing, what messages are coming up, and so on.

How does that sound to you? What day/times would you be available? What time zone are you in (I'm in Atlantic (AST))?

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Wednesday, June 26, 2024 6:04 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim -

Just to confirm - I downloaded the related_1.0.tar.gz that indicates it is for R 3.5 - that is the only install file I see at https://github.com/timothyfrasier/related.

I uninstalled related using remove.packages()

I had both Rtools 4.3 and 4.4 installed, but at your suggestion I uninstalled 4.4 thinking that would force R to use Rtools 4.3. But that just caused the compilation of related to exit with non-zero status. I reinstalled Rtools4.4 and installed related_1.0.tar.gz through r studio using the local file.

I get these messages and a normal exit - I don't see any errors - perhaps you can see something that I don't.

Installing package into ‘C:/Users/mneel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified)

  • installing source package 'related' ... using staged installation libs using C compiler: 'gcc.exe (GCC) 13.2.0' using Fortran compiler: 'GNU Fortran (GCC) 13.2.0' gcc -I"C:/PROGRA1/R/R-441.1/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c family_sim.c -o family_sim.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c related.f90 -o related.o gcc -shared -s -static-libgcc -o related.dll tmp.def family_sim.o related.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LC:/PROGRA1/R/R-441.1/bin/x64 -lR installing to C:/Users/mneel/AppData/Local/R/win-library/4.4/00LOCK-related/00new/related/libs/x64

R data byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path

  • DONE (related)

library(related) indicates all is well

library(related) Loading required package: tools Loading required package: ggplot2

But loading and running the code in the tutorial for you test data set still crashes R with a fatal error.

— Reply to this email directly, view it on GitHub< https://github.com/timothyfrasier/related/issues/12#issuecomment-2192624222>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AA3NYWMCAAYQINS4AWAGAZDZJMUFVAVCNFSM6AAAAABJOEANBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJSGYZDIMRSGI>.

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timothyfrasier commented 1 month ago

Hi:

Okay great, can you send me a direct email (not via Github), and we can plan it @.***). Again, what time zone are you in?

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Friday, June 28, 2024 1:01 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

That would be WONDERFUL!!!!! I really really appreciate it. I am available today or anytime next week except Monday morning.

On Fri, Jun 28, 2024 at 11:51 AM timothyfrasier @.***> wrote:

Hi:

This is so strange. I wonder if having a Zoom call next week (or sometime soon) would be a good idea. That way I can see exactly what you are typing, what messages are coming up, and so on.

How does that sound to you? What day/times would you be available? What time zone are you in (I'm in Atlantic (AST))?

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: mneel @.> Sent: Wednesday, June 26, 2024 6:04 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] coancestry crashing R on Windows (Issue #12)

Hi Tim -

Just to confirm - I downloaded the related_1.0.tar.gz that indicates it is for R 3.5 - that is the only install file I see at https://github.com/timothyfrasier/related.

I uninstalled related using remove.packages()

I had both Rtools 4.3 and 4.4 installed, but at your suggestion I uninstalled 4.4 thinking that would force R to use Rtools 4.3. But that just caused the compilation of related to exit with non-zero status. I reinstalled Rtools4.4 and installed related_1.0.tar.gz through r studio using the local file.

I get these messages and a normal exit - I don't see any errors - perhaps you can see something that I don't.

Installing package into ‘C:/Users/mneel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified)

  • installing source package 'related' ... using staged installation libs using C compiler: 'gcc.exe (GCC) 13.2.0' using Fortran compiler: 'GNU Fortran (GCC) 13.2.0' gcc -I"C:/PROGRA1/R/R-441.1/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c family_sim.c -o family_sim.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c related.f90 -o related.o gcc -shared -s -static-libgcc -o related.dll tmp.def family_sim.o related.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LC:/PROGRA1/R/R-441.1/bin/x64 -lR installing to C:/Users/mneel/AppData/Local/R/win-library/4.4/00LOCK-related/00new/related/libs/x64

R data byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path

  • DONE (related)

library(related) indicates all is well

library(related) Loading required package: tools Loading required package: ggplot2

But loading and running the code in the tutorial for you test data set still crashes R with a fatal error.

— Reply to this email directly, view it on GitHub< https://github.com/timothyfrasier/related/issues/12#issuecomment-2192624222>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AA3NYWMCAAYQINS4AWAGAZDZJMUFVAVCNFSM6AAAAABJOEANBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJSGYZDIMRSGI>.

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