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geomorphR / geomorph

Geomorph is a software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment. This repository is dedicated to providing stable and beta versions between CRAN uploads
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readmulti.nts Function Issues #33

Closed rachsglee23 closed 3 years ago

rachsglee23 commented 3 years ago

Hello! I am a student relatively new to R hoping to use the "geomorph" package in order run a morphometric analysis of landmarked heads from microCT scans. We are trying to utilize the "readmulti.nts" function but have had some issues with the recent package version. I would greatly appreciate any guidance on how to solve this issue!

We were able to use geomorph version 3.3.1 to run the code attached below, however the updated 4.0.0 version of geomorph with the readmulti.nts function as a wrapper for the readland.nts function no longer allows for our code to work. Specifically, the readmulti.nts function is no longer compiling the nts files into a list with the correct dimensions (we are expecting to see 22 3 117, however, we continue to see 1 3 2552).

Screen Shot 2021-06-10 at 4 44 32 PM Screen Shot 2021-06-10 at 4 49 54 PM
deanadams commented 3 years ago

This topic was covered a few weeks ago. If you install a new version of geomorph from GitHub, it should resolve the problem.

Best,

Deam

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From: rachsglee23 @.> Sent: Thursday, June 10, 2021 3:53:23 PM To: geomorphR/geomorph @.> Cc: Subscribed @.***> Subject: [geomorphR/geomorph] readmulti.nts Function Issues (#33)

Hello! I am a student relatively new to R hoping to use the "geomorph" package in order run a morphometric analysis of landmarked heads from microCT scans. We are trying to utilize the "readmulti.nts" function but have had some issues with the recent package version. I would greatly appreciate any guidance on how to solve this issue!

We were able to use geomorph version 3.3.1 to run the code attached below, however the updated 4.0.0 version of geomorph with the readmulti.nts function as a wrapper for the readland.nts function no longer allows for our code to work. Specifically, the readmulti.nts function is no longer compiling the nts files into a list with the correct dimensions (we are expecting to see 22 3 117, however, we continue to see 1 3 2552).

[Screen Shot 2021-06-10 at 4 44 32 PM]https://user-images.githubusercontent.com/85316304/121594491-23dbf200-ca0b-11eb-854d-c11bfddfc020.png

[Screen Shot 2021-06-10 at 4 49 54 PM]https://user-images.githubusercontent.com/85316304/121595062-e75cc600-ca0b-11eb-9139-e01c469a0ae3.png

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rachsglee23 commented 3 years ago

Thank you for the prompt response. I followed the instructions to install the newest version of geomorph from GitHub as stated here: https://github.com/geomorphR/geomorph However, when doing so the error message below continues to pop up. Any guidance or suggestions would be greatly appreciated!

Screen Shot 2021-06-11 at 10 53 28 AM
deanadams commented 3 years ago

Sorry One also needs to install the latest RRPP from GitHub. My apologies for the omission.

Dean

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From: rachsglee23 @.> Sent: Friday, June 11, 2021 9:56:53 AM To: geomorphR/geomorph @.> Cc: Adams, Dean [EEOB] @.>; Comment @.> Subject: Re: [geomorphR/geomorph] readmulti.nts Function Issues (#33)

Thank you for the prompt response. I followed the instructions to install the newest version of geomorph from GitHub as stated here: https://github.com/geomorphR/geomorph However, when doing so the error message below continues to pop up. Any guidance or suggestions would be greatly appreciated!

[Screen Shot 2021-06-11 at 10 53 28 AM]https://user-images.githubusercontent.com/85316304/121706068-47527b80-caa3-11eb-9bc4-a6a4cd2b5012.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/geomorphR/geomorph/issues/33#issuecomment-859640504, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABSK7KM2472R4BG6OOW7U2DTSIP3LANCNFSM46PLGELA.

rachsglee23 commented 3 years ago

Unfortunately, in order to install the latest RRPP from GitHub I require the package Matrix to be installed first. I am having trouble installing this package to R -- it continues to ask for approval to use compilers, to which I've installed XCode as well as gfortran (which I confirmed installed correctly by running the hello.f90 test in terminal). However, install.packages("Matrix") results in non-zero status. When I try installing from source (downloading the tar.gz file and installing from Tools in R), it installs however it will not load using library(Matrix).

mlcollyer commented 3 years ago

The compilers are not part of RRPP or geomorph package requirements. I’m afraid you will have to sort that out with the package that is giving you trouble. In the past I have had some success rebooting after updating Xcode. I have also had some success reinstalling R after having compilation issues. But this has been resolving by trial and error.

Sorry to not have better advice.

Mike

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On Jun 14, 2021, at 8:01 PM, rachsglee23 @.***> wrote:

 Unfortunately, in order to install the latest RRPP from GitHub I require the package Matrix to be installed first. I am having trouble installing this package to R -- it continues to ask for approval to use compilers, to which I've installed XCode as well as gfortran (which I confirmed installed correctly by running the hello.f90 test in terminal). However, install.packages("Matrix") results in non-zero status. When I try installing from source (downloading the tar.gz file and installing from Tools in R), it installs however it will not load using library(Matrix).

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rachsglee23 commented 3 years ago

Thank you for all of your help! Below I have attached my troubleshooting methods for this issue that solved my problem should anyone need it as a resource.

What to do when “geomorph” will not load the proper packages