Install Request: ImageMagick [06588070] [06588578] [06533912]

[kaibinary]

Application: ImageMagick

Link: https://imagemagick.org/script/download.php

Cluster: Myriad

Description: A dependency for GSVA and imcRtools

License: https://imagemagick.org/script/license.php

[kaibinary]

First install ImageMagick 7.1.1-31 and then set the shell environment variables.

module load r/4.3.3-openblas/gnu-10.2.0
wget https://github.com/ImageMagick/ImageMagick/archive/refs/tags/7.1.1-31.tar.gz
tar -xf 7.1.1-31.tar.gz
cd ImageMagick-7.1.1-31
./configure --prefix=${HOME}/imagemagick/7.1.1-31
make -j4
make install

INCLUDE_PATH=$INCLUDE_PATH:~/imagemagick/7.1.1-31/include
PKG_CONFIG_PATH=$PKG_CONFIG_PATH:~/imagemagick/7.1.1-31/lib/pkgconfig
LIBRARY_PATH=$LIBRARY_PATH:~/imagemagick/7.1.1-31/lib
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/imagemagick/7.1.1-31/lib

For escape, start R interactively and run the following in sequence (using default path for personal library, etc.);

install.packages("remotes")
library(remotes)
install_github("rcastelo/GSVA")
install_version("Matrix", version = "1.6-5")
install_github("ncborcherding/escape")

For imcRtools, start R interactively and run the following in sequence (using default path for personal library, etc.);

install.packages("BiocManager")
BiocManager::install("imcRtools")

The personal R library path is located in;

{HOME}/R/x86_64-pc-linux-gnu-library/4.3

[balston]

I will make a build script and do a central install on the Clusters starting with Myriad.

[balston]

Build script done and running on Myriad from the ccspapp account:

./ImageMagick-7.1.1_install 2>&1 | tee ~/Scratch/ImageMagick/ImageMagick-7.1.1_install.log

[balston]

the build script has run without errors. Need to create a module file next and then test with R

[balston]

I've found an error in the build and so need to fix the build script and rerun

[balston]

OK ImageMagick is now working standalone. Tomorrow will test with our R bundle.

[balston]

Test looks ok:

module unload compilers mpi gcc-libs
module load r/r-4.3.3_bc-3.18
 module load imagemagick/7.1.1/gnu-10.2.0
[ccaabaa@login13 ~]$ R

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages ('magick')
Installing package into ‘/lustre/home/ccaabaa/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/magick_2.8.3.tar.gz'
Content type 'application/x-gzip' length 4600396 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

* installing *source* package ‘magick’ ...

** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (magick)

[balston]

users have already been informed.

[balston]

now install on all clusters:

• [x] Kathleen
• [x] Michael
• [x] Myriad
• [x] Young