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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
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ANTsRCore, colormap and v8 #270

Closed nadluru closed 4 years ago

nadluru commented 5 years ago

Dear ANTsR team,

I am trying to install ANTsR using R CMD INSTALL approach. I can get the ITKR installed from the source, ANTsRCore but only from binary (ANTsRCore_0.6.3.2_R_x86_64-pc-linux-gnu_R3.5.tar.gz) and then when I try to install ANTsR it says ANTsRCore could not be loaded because of missing colormap package which internally depends on v8 both of which I could get installed. I assumed if I installed ANTsRCore from binary I wouldn't have to install the colormap and v8 but that seems incorrect.

Overall the dependency on colormap and v8 seems to be main issue. Could you kindly advice on how best to proceed with the ANTsRCore installation?

The main error message from ANTsR installation is below.

Error: package or namespace load failed for ‘ANTsRCore’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), v ersionCheck = vI[[j]]): there is no package called ‘colormap’ Error : package ‘ANTsRCore’ could not be loaded ERROR: lazy loading failed for package ‘ANTsR’ * removing ‘/home/adluru/R/x86_64-redhat-linux-gnu-library/3.5/ANTsR’

Thank you so much for your help. Sincerely, Nagesh

ntustison commented 5 years ago

I personally find the devtools::install_github( "..." ) route to be easiest for ITKR, ANTsRCore, and ANTsR.

dorianps commented 5 years ago

Just throwing it there, did you try installing V8-devel ?

On Tue, Apr 16, 2019, 5:25 PM Nick Tustison notifications@github.com wrote:

I personally find the devtools::install_github( "..." ) route to be easiest for ITKR, ANTsRCore, and ANTsR.

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stnava commented 5 years ago

reference this: https://github.com/ANTsX/ANTsRCore/blob/master/.travis.yml

nadluru commented 5 years ago

Thank you all for your prompt suggestions. The main problem in any of the ways (including that from a binary) seems to be getting the V8 installed and loaded properly. I can't seem to be able to install the v8-devel without sudo. I am going to ask our IT to do it and report back how it goes. Thank you all again!

stnava commented 5 years ago

@muschellij2 has also suggested that the colormap / V8 dependency is not worth the pain it causes. to resolve, someone would have to either:

and/or

nadluru commented 5 years ago

Dear team,

Sorry for the delay in my update. So our IT said it got the v8 and v8-devel installed. I can rpm query them (screenshot below). v8installed

I also added /usr/lib64 to LD_LIBRARY_PATH. In my rpm query I could not find /usr/include/v8-3.14 though which I see in the error message (screenshot below) when I tried to install ANTsRCore using

devtools::install_github('stnava/ANTsRCore', lib='/home/adluru/R/x86_64-redhat-linux-gnu-library/3.5/')

v8error

What would be your recommendation be for next trials in getting the ANTsRCore installed on our servers. I see the previous comment was potentially to make v8 optional. Would it be easy enough for you to do this?

Thanks again for all your help and apologies for the delay in getting the update posted (weekends are not what they used to be for me in my early days of research).

Sincerely, Nagesh

muschellij2 commented 5 years ago

This is something to bring up to https://github.com/jeroen/V8 John

On Mon, Apr 22, 2019 at 11:21 AM Nagesh Adluru notifications@github.com wrote:

Dear team,

Sorry for the delay in my update. So our IT said it got the v8 and v8-devel installed. I can rpm query them (screenshot below). [image: v8installed] https://user-images.githubusercontent.com/5951009/56507577-6074c880-64e7-11e9-8411-4f282b42a2cc.png

I also added /usr/lib64 to LD_LIBRARY_PATH. In my rpm query I could not find /usr/include/v8-3.14 though which I see in the error message (screenshot below) when I tried to install ANTsRCore using

devtools::install_github('stnava/ANTsRCore', lib='/home/adluru/R/x86_64-redhat-linux-gnu-library/3.5/')

[image: v8error] https://user-images.githubusercontent.com/5951009/56507643-9154fd80-64e7-11e9-8b2a-3a536afa66a1.png

What would be your recommendation be for next trials in getting the ANTsRCore installed on our servers. I see the previous comment was potentially to make v8 optional. Would it be easy enough for you to do this?

Thanks again for all your help and apologies for the delay in getting the update posted (weekends are not what they used to be for me in my early days of research).

Sincerely, Nagesh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/270#issuecomment-485447808, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIGPLSCWNRLGTFON5TC7F3PRXJWXANCNFSM4HGOUV7Q .

muschellij2 commented 5 years ago

Also - likely something in LD_LIBRARY_PATH or other paths. John

On Mon, Apr 22, 2019 at 11:22 AM John Muschelli muschellij2@gmail.com wrote:

This is something to bring up to https://github.com/jeroen/V8 John

On Mon, Apr 22, 2019 at 11:21 AM Nagesh Adluru notifications@github.com wrote:

Dear team,

Sorry for the delay in my update. So our IT said it got the v8 and v8-devel installed. I can rpm query them (screenshot below). [image: v8installed] https://user-images.githubusercontent.com/5951009/56507577-6074c880-64e7-11e9-8411-4f282b42a2cc.png

I also added /usr/lib64 to LD_LIBRARY_PATH. In my rpm query I could not find /usr/include/v8-3.14 though which I see in the error message (screenshot below) when I tried to install ANTsRCore using

devtools::install_github('stnava/ANTsRCore', lib='/home/adluru/R/x86_64-redhat-linux-gnu-library/3.5/')

[image: v8error] https://user-images.githubusercontent.com/5951009/56507643-9154fd80-64e7-11e9-8b2a-3a536afa66a1.png

What would be your recommendation be for next trials in getting the ANTsRCore installed on our servers. I see the previous comment was potentially to make v8 optional. Would it be easy enough for you to do this?

Thanks again for all your help and apologies for the delay in getting the update posted (weekends are not what they used to be for me in my early days of research).

Sincerely, Nagesh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/270#issuecomment-485447808, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIGPLSCWNRLGTFON5TC7F3PRXJWXANCNFSM4HGOUV7Q .

muschellij2 commented 5 years ago

Try simply install.packages("V8") and see the same result. John

On Mon, Apr 22, 2019 at 11:23 AM John Muschelli muschellij2@gmail.com wrote:

Also - likely something in LD_LIBRARY_PATH or other paths. John

On Mon, Apr 22, 2019 at 11:22 AM John Muschelli muschellij2@gmail.com wrote:

This is something to bring up to https://github.com/jeroen/V8 John

On Mon, Apr 22, 2019 at 11:21 AM Nagesh Adluru notifications@github.com wrote:

Dear team,

Sorry for the delay in my update. So our IT said it got the v8 and v8-devel installed. I can rpm query them (screenshot below). [image: v8installed] https://user-images.githubusercontent.com/5951009/56507577-6074c880-64e7-11e9-8411-4f282b42a2cc.png

I also added /usr/lib64 to LD_LIBRARY_PATH. In my rpm query I could not find /usr/include/v8-3.14 though which I see in the error message (screenshot below) when I tried to install ANTsRCore using

devtools::install_github('stnava/ANTsRCore', lib='/home/adluru/R/x86_64-redhat-linux-gnu-library/3.5/')

[image: v8error] https://user-images.githubusercontent.com/5951009/56507643-9154fd80-64e7-11e9-8b2a-3a536afa66a1.png

What would be your recommendation be for next trials in getting the ANTsRCore installed on our servers. I see the previous comment was potentially to make v8 optional. Would it be easy enough for you to do this?

Thanks again for all your help and apologies for the delay in getting the update posted (weekends are not what they used to be for me in my early days of research).

Sincerely, Nagesh

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/270#issuecomment-485447808, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIGPLSCWNRLGTFON5TC7F3PRXJWXANCNFSM4HGOUV7Q .

nadluru commented 5 years ago

This is something to bring up to https://github.com/jeroen/V8 John

I just submitted an issue there as well.

Also - likely something in LD_LIBRARY_PATH or other paths. John

I did update LD_LIBRARY_PATH to include /usr/lib64 which is where the v8 libraries seem to have been installed (you can see that from the first screenshot in my previous comment).

Try simply install.packages("V8") and see the same result. John

Same result with the same error message!

hassaanmahmood commented 5 years ago

@nadluru hi, did you solve your problem? I am also getting same error sudo R CMD INSTALL ANTsRCore

thanks

hassaanmahmood commented 5 years ago

I solved this issue by doing this

sudo apt-get install libcurl4-openssl-dev libssl-dev if(!require("V8")) install.packages("V8") if(!require("devtools")) install.packages("devtools") devtools::install_github("bhaskarvk/colormap") sudo R CMD INSTALL ANTsRCore

nadluru commented 5 years ago

@hassaanmahmood Thanks for reporting your solution, but I am not sure if this will work for RHEL 7. I don't have sudo privileges to test this myself and I will bring it up with our IT.

stnava commented 5 years ago

I removed the dependency on colormap/V8 with a recent commit. fewer colormap options but still several good options via viridis.