errors when running fit_ssm in animotum about animotum

[ianjonsen]

Hi Belinda, Thanks for providing your code & data. I have run your code but am unable to reproduce the model fitting errors you got. So, I'm wondering if you're using an older version of aniMotum - latest version is 1.2, which was released on 06/11/23. If you have an older version then I'd try updating and re-running your code. You can install from r-universe like this:

install.packages("aniMotum", 
                 repos = c("https://cloud.r-project.org",
                 "https://ianjonsen.r-universe.dev"),
                 dependencies = TRUE, build_vignettes = TRUE)

If you do have v 1.2 installed then (for reasons currently unknown to me) you probably should update to the latest R version.

[BelindaCannell]

Hi Ian Thanks for your email. I did have the latest version of aniMotum. I have now tried using R version 4.2.3, and have to reinstall everything. Unfortunately now I am getting errors during the installation e.g. * installing *source* package 'jsonlite' ... ** package 'jsonlite' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"C:/PROGRA~1/R/R-42~1.3/include" -DNDEBUG -Iyajl/api -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o /bin/sh: line 1: gcc: command not found make: *** [C:/PROGRA~1/R/R-42~1.3/etc/x64/Makeconf:253: base64.o] Error 127 ERROR: compilation failed for package 'jsonlite' * removing 'C:/Program Files/R/R-4.2.3/library/jsonlite' Warning in install.packages : installation of package ‘jsonlite’ had non-zero exit status * installing *source* package 'tmvtnorm' ... ** package 'tmvtnorm' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"C:/PROGRA~1/R/R-42~1.3/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Fortran2CWrapper.c -o Fortran2CWrapper.o /bin/sh: line 1: gcc: command not found make: *** [C:/PROGRA~1/R/R-42~1.3/etc/x64/Makeconf:253: Fortran2CWrapper.o] Error 127 ERROR: compilation failed for package 'tmvtnorm' * removing 'C:/Program Files/R/R-4.2.3/library/tmvtnorm' Warning in install.packages : installation of package ‘tmvtnorm’ had non-zero exit status Aargh, I hate R sometimes. I am now waiting for the uni IT guys to help me☹ I’ll let you know how I get on. Cheers Belinda From: Ian Jonsen ***@***.***> Sent: Thursday, 7 December 2023 1:27 AM To: ianjonsen/aniMotum ***@***.***> Cc: Belinda Cannell ***@***.***>; Author ***@***.***> Subject: Re: [ianjonsen/aniMotum] errors when running fit_ssm in animotum (Issue #47) Hi Belinda, Thanks for providing your code & data. I have run your code but am unable to reproduce the model fitting errors you got. So, I'm wondering if you're using an older version of aniMotum - latest version is 1.2, which was released on 06/11/23. If you have an older version then I'd try updating and re-running your code. You can install from r-universe like this: install.packages("aniMotum", repos = c("https://cloud.r-project.org", "https://ianjonsen.r-universe.dev"), dependencies = TRUE, build_vignettes = TRUE) If you do have v 1.2 installed then (for reasons currently unknown to me) you probably should update to the latest R version. — Reply to this email directly, view it on GitHub<#47 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIAXI67HCNBGTRZ6GZMW3QDYICTHLAVCNFSM6AAAAABAHGKRK6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBTGM2DCNZTG4>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[ianjonsen]

Sorry to hear that - it can be a royal pain at times. If you’ve got a Windows machine, you’ll have to install RTools to be able to compile packages that rely on C++ code. You can get RTools here: https://cran.r-project.org/

[BelindaCannell]

Hi Ian Thanks for your email. I already have Rtools installed ☹ Yes it can be a pain, and more so when you have a new laptop and having to install bespoke software. Never an easy task. Hopefully today IT will contact me! A quick question though- will aniMotum work for a single day trip with few sat tag locations? Cheers Belinda From: Ian Jonsen ***@***.***> Sent: Thursday, 7 December 2023 10:26 PM To: ianjonsen/aniMotum ***@***.***> Cc: Belinda Cannell ***@***.***>; Author ***@***.***> Subject: Re: [ianjonsen/aniMotum] errors when running fit_ssm in animotum (Issue #47) Sorry to hear that - it can be a royal pain at times. If you’ve got a Windows machine, you’ll have to install RTools to be able to compile packages that rely on C++ code. You can get RTools here: https://cran.r-project.org/ — Reply to this email directly, view it on GitHub<#47 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIAXI65CQAYQDFUI6GNRWKDYIHGVZAVCNFSM6AAAAABAHGKRK6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBVGQZTKMJTGQ>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[BelindaCannell]

Hi Ian Now I am getting this message: Loading required package: aniMotum Warning messages: 1: In checkMatrixPackageVersion(getOption("TMB.check.Matrix", TRUE)) : Package version inconsistency detected. TMB was built with Matrix version 1.6.4 Current Matrix version is 1.5.3 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package 2: In checkTMBPackageVersion() : Package version inconsistency detected. aniMotum was built with TMB version 1.9.6 Current TMB version is 1.9.9 Please re-install 'aniMotum' from source using install.packages('aniMotum', type = 'source') or remove your current TMB version and re-install using remotes::install_version('TMB', version = '1.9.6') Any suggestions as to what I should do with the TMB? Cheers Belinda From: Ian Jonsen ***@***.***> Sent: Thursday, 7 December 2023 10:26 PM To: ianjonsen/aniMotum ***@***.***> Cc: Belinda Cannell ***@***.***>; Author ***@***.***> Subject: Re: [ianjonsen/aniMotum] errors when running fit_ssm in animotum (Issue #47) Sorry to hear that - it can be a royal pain at times. If you've got a Windows machine, you'll have to install RTools to be able to compile packages that rely on C++ code. You can get RTools here: https://cran.r-project.org/ - Reply to this email directly, view it on GitHub<#47 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIAXI65CQAYQDFUI6GNRWKDYIHGVZAVCNFSM6AAAAABAHGKRK6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBVGQZTKMJTGQ>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[BelindaCannell]

Hi Ian I have now sorted this error by removing TMB 1.9.9 and installing 1.9.6 Cheers Belinda From: Belinda Cannell Sent: Friday, 8 December 2023 3:24 PM To: ianjonsen/aniMotum ***@***.***> Subject: RE: [ianjonsen/aniMotum] errors when running fit_ssm in animotum (Issue #47) Hi Ian Now I am getting this message: Loading required package: aniMotum Warning messages: 1: In checkMatrixPackageVersion(getOption("TMB.check.Matrix", TRUE)) : Package version inconsistency detected. TMB was built with Matrix version 1.6.4 Current Matrix version is 1.5.3 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package 2: In checkTMBPackageVersion() : Package version inconsistency detected. aniMotum was built with TMB version 1.9.6 Current TMB version is 1.9.9 Please re-install 'aniMotum' from source using install.packages('aniMotum', type = 'source') or remove your current TMB version and re-install using remotes::install_version('TMB', version = '1.9.6') Any suggestions as to what I should do with the TMB? Cheers Belinda From: Ian Jonsen ***@***.******@***.***>> Sent: Thursday, 7 December 2023 10:26 PM To: ianjonsen/aniMotum ***@***.******@***.***>> Cc: Belinda Cannell ***@***.******@***.***>>; Author ***@***.******@***.***>> Subject: Re: [ianjonsen/aniMotum] errors when running fit_ssm in animotum (Issue #47) Sorry to hear that - it can be a royal pain at times. If you've got a Windows machine, you'll have to install RTools to be able to compile packages that rely on C++ code. You can get RTools here: https://cran.r-project.org/ - Reply to this email directly, view it on GitHub<#47 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIAXI65CQAYQDFUI6GNRWKDYIHGVZAVCNFSM6AAAAABAHGKRK6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBVGQZTKMJTGQ>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[BelindaCannell]

HI Ian So the great news is that I have aniMotum working on my PC, but unfortunately not my work laptop, likely due to stupid lack of admin rights!!! Cheers Belinda From: Ian Jonsen ***@***.***> Sent: Thursday, 7 December 2023 10:26 PM To: ianjonsen/aniMotum ***@***.***> Cc: Belinda Cannell ***@***.***>; Author ***@***.***> Subject: Re: [ianjonsen/aniMotum] errors when running fit_ssm in animotum (Issue #47) Sorry to hear that - it can be a royal pain at times. If you've got a Windows machine, you'll have to install RTools to be able to compile packages that rely on C++ code. You can get RTools here: https://cran.r-project.org/ - Reply to this email directly, view it on GitHub<#47 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIAXI65CQAYQDFUI6GNRWKDYIHGVZAVCNFSM6AAAAABAHGKRK6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBVGQZTKMJTGQ>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[ianjonsen]

Yikes, what a pain! At least you have it installed & working somewhere! Answer to your track question: You can fit to relatively short tracks, eg shorter than a day, but it all depends on how many locations you have & the time step you choose. eg. < 10-15 locations would be very challenging to estimate something sensible. If your track(s) are about a day long then you probably don't want to use a time step longer than an hour or so.