Packages Installation

[maiqnguyen]

Hi, I would like to ask for support in packages installation.
I'm having trouble installing the below packages:
devtools::install_github("stnava/ITKR")
devtools::install_github("stnava/ANTsR")
devtools::install_github("muschellij2/extrantsr")

I have been advised to install CMake so I have CMake 3.31.3 installed and the package cmaker is also installed, but I still encounter errors upon the above packages installation.
My operating system is masOS Big Sur 11.7.10

I would really appreciate further advice.
Thank you.

[cookpa]

I haven't used devtools in a long time. This works for me

git clone https://github.com/ANTsX/ITKR
R CMD INSTALL ./ITKR

Note that you need a clean install, trying to run on a previously configured directory will fail.

This will only work if you have the Mac OS "command line developer tools" installed. You can check this with

pkgutil --pkg-info=com.apple.pkg.CLTools_Executables 

[maiqnguyen]

Thank you for your suggestions. I have tried, but the below error occured.

I have installed CMake 3.31.3 but in the error message it is different.
I don't know what is the problem and how to solve.

[cookpa]

If you installed cmaker, remove it. It will use an old cmake. Once that is gone, the ITKR installer should use the system cmake

[maiqnguyen]

I removed cmaker, cleaned the existing ITKR directory (from previous failed installation) and tried to install ITKR again.
This time it ran longer and seemed working, but in the end the below error occurred.

[cookpa]

I'm not sure where it's getting this cmake version. What happens if you type

which cmake

and then

cmake --version

[maiqnguyen]

It seems like cmake could not be found despite the fact that I installed it.
How can I solve this problem?

[cookpa]

You need to add its location to the PATH

[maiqnguyen]

Sorry Philip, could you be more specific. I'm not familiar with this in general.
Thank you.

[maiqnguyen]

I think I managed to do what has been suggested.
The CMake version seems fine...

[cookpa]

https://stackoverflow.com/questions/11530090/adding-a-new-entry-to-the-path-variable-in-zsh

Verify by opening a new terminal and doing cmake --version

[cookpa]

I think I managed to do what has been suggested.

The CMake version seems fine...

This will only work for the current shell, please see the link above

[maiqnguyen]

I tried with the PATH thing, but I think I have not succeeded.
On the other hand I noticed that when ever I tried to install ITKR, it automatically installs cmaker version 3.11.4
Might this be the problem?

[cookpa]

Yes, it's definitely a problem. If it's trying to install cmaker, that means it's not finding cmake.

[maiqnguyen]

Do you have any suggestions on how to solve this problem?
If it is the setting of the PATH, I will try again, but if you could give a more detailed description would be very helpful.
Many thanks.

[cookpa]

The PATH needs to be set and exported, in your ~/.zshrc file:

export PATH="/wherever/cmake/is/bin:$PATH"

Then close the terminal and open a new one. Immediately type

cmake --version

If that works, then you can try to cd to where your cloned code is and do R CMD INSTALL ITKR.