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ANTsRCore, colormap and v8 #270

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nadluru opened this issue Apr 16, 2019 · 14 comments
Closed

ANTsRCore, colormap and v8 #270

nadluru opened this issue Apr 16, 2019 · 14 comments

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@nadluru
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nadluru commented Apr 16, 2019

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

@dorianps
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dorianps commented Apr 16, 2019 via email

@stnava
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stnava commented Apr 16, 2019

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

@nadluru
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nadluru commented Apr 17, 2019

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
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stnava commented Apr 17, 2019

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

    1. refactor the dependency such that it is optional

and/or

    1. refactor plot.antsImage st we can still use interesting colormaps pretty easily w/o requiring v8

@nadluru
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nadluru commented Apr 22, 2019

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
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muschellij2 commented Apr 22, 2019 via email

@muschellij2
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muschellij2 commented Apr 22, 2019 via email

@muschellij2
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muschellij2 commented Apr 22, 2019 via email

@nadluru nadluru mentioned this issue Apr 22, 2019
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@nadluru
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nadluru commented Apr 22, 2019

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

  • installing to library ‘/home/hassan/R/x86_64-pc-linux-gnu-library/3.4’
    ERROR: dependency ‘colormap’ is not available for package ‘ANTsRCore’

thanks

@hassaanmahmood
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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
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nadluru commented May 16, 2019

@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
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stnava commented May 17, 2019

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

@stnava stnava closed this as completed May 9, 2020
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6 participants
@stnava @ntustison @muschellij2 @nadluru @dorianps @hassaanmahmood