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timothyfrasier / related

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A few functions crash R on Windows #14

Open AGibsonV opened 1 year ago

AGibsonV commented 1 year ago

Hi Tim,

A colleague recommended your package and I've installed in according to the tutorial instructions. I'm following a r script that a previous colleague wrote to get some simple related estimates (i.e. the script produced the results needed). My dataset consists of 47 individuals and 32 loci. When trying to run functions such as compareestimators() and coancestry() R terminates with the time bomb aborted session message, with no other information.

I tested these functions on the GenotypeData which comes with the package, and compareestimators() works without a problem however coancestry() crashes too which makes me think it isn't just a problem with my data input. Regardless, I double checked the data inputs but the formatting and the read-in of the data is the same as the sample data provided by related.

I am running the script under: R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) I am running R within RStudio 2022.12.0 Build 353

Any help is greatly appreciated. This package seems like the perfect simple solution to my genetic related analysis needs!

All the best,

Aline

timothyfrasier commented 1 year ago

Hi Aline:

I'm sorry that related is giving you trouble. Unfortunately, I have all-day meetings every day this week. However, I will take a look at this next week and get back to you.

-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: AGibsonV @.> Sent: Thursday, March 16, 2023 3:36 AM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] A few functions crash R on Windows (Issue #14)

Hi Tim,

A colleague recommended your package and I've installed in according to the tutorial instructions. I'm following a r script that a previous colleague wrote to get some simple related estimates (i.e. the script produced the results needed). My dataset consists of 47 individuals and 32 loci. When trying to run functions such as compareestimators() and coancestry() R terminates with the time bomb aborted session message, with no other information.

I tested these functions on the GenotypeData which comes with the package, and compareestimators() works without a problem however coancestry() crashes too which makes me think it isn't just a problem with my data input. Regardless, I double checked the data inputs but the formatting and the read-in of the data is the same as the sample data provided by related.

I am running the script under: R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) I am running R within RStudio 2022.12.0 Build 353

Any help is greatly appreciated. This package seems like the perfect simple solution to my genetic related analysis needs!

All the best,

Aline

— Reply to this email directly, view it on GitHubhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftimothyfrasier%2Frelated%2Fissues%2F14&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Cd379094c6f9c42eacd7a08db25e8d5cc%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638145454170752733%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=kbXxlxVeL8hIKy3sS%2F3%2BL3Iy07vmijdf3JqShDNw6Kg%3D&reserved=0, or unsubscribehttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAA3NYWIBL7RLO23AUEHSD33W4KYINANCNFSM6AAAAAAV4Y72SU&data=05%7C01%7Ctimothy.frasier%40smu.ca%7Cd379094c6f9c42eacd7a08db25e8d5cc%7C060b02ae57754360abbae2e29cca6627%7C1%7C0%7C638145454170752733%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=eUvods1qzA0ZOcvcEFD4Byd67c6imAWguG%2F3pyh9rso%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

ac-harris commented 1 year ago

Hi, Tim--

Has this issue been resolved? I'm trying to run the coancestry function with the GenotypeData object from the package and get the same error as Aline. I'm running R version 4.2.2, platform x86_64-w64-mingw32/x64 (64-bit), and Rstudio 2023.03.0 Build 386.

Thanks for any guidance you can provide! Audrey

timothyfrasier commented 1 year ago

Hi Audrey:

I just updated my version of R (to 4.2.3) and installed related, and it is working fine. I am on a Linux machine though. Are you on Windows? If so, I will find a Windows computer, update R, and try it out there.

-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: Audrey Harris @.> Sent: Wednesday, April 12, 2023 1:59 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] A few functions crash R on Windows (Issue #14)

Hi, Tim--

Has this issue been resolved? I'm trying to run the coancestry function with the GenotypeData object from the package and get the same error as Aline. I'm running R version 4.2.2, platform x86_64-w64-mingw32/x64 (64-bit), and Rstudio 2023.03.0 Build 386.

Thanks for any guidance you can provide! Audrey

— Reply to this email directly, view it on GitHubhttps://github.com/timothyfrasier/related/issues/14#issuecomment-1505615264, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA3NYWK7Z23LGFW3QSCCR5DXA3NNZANCNFSM6AAAAAAV4Y72SU. You are receiving this because you commented.Message ID: @.***>

ac-harris commented 1 year ago

Hi, Tim--

I am using a windows computer. I was able to revert back to an earlier version of R (4.1.2) and get the function working, but it seems like the windows version of 4.2.2 is where the problem lies.

Thanks! Audrey

timothyfrasier commented 1 year ago

Hi Audrey:

Ok, thanks for that information. I’ll see what I can do tomorrow.

-Tim

Sent from my iPhone

On Apr 13, 2023, at 4:26 PM, Audrey Harris @.***> wrote:



Hi, Tim--

I am using a windows computer. I was able to revert back to an earlier version of R (4.1.2) and get the function working, but it seems like the windows version of 4.2.2 is where the problem lies.

Thanks! Audrey

— Reply to this email directly, view it on GitHubhttps://github.com/timothyfrasier/related/issues/14#issuecomment-1507500377, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA3NYWPE6KVMT6GSQDRABKLXBBHP5ANCNFSM6AAAAAAV4Y72SU. You are receiving this because you commented.Message ID: @.***>

neellab-umd commented 1 year ago

Hi Tim -

I am still having this same problem on my Windows machine. It has happened with multiple versions of R, the latest being 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts".

Specifically for me, the coancestry() function crashes R on both my data and your test data. Have you been able to track down the problem? In case it helps, the crash happens only after the function has run for a long time. So perhaps it is something in how the results of coancestry() are written to an object at the end of the operations.