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heroalone / Garfield

Garfield: Genetic Association by Random Forest and InterpretivE Logic Decisions.
GNU Affero General Public License v3.0
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problems with install #1

Closed Vallebueno closed 1 week ago

Vallebueno commented 4 months ago

No instances of Garfield to run after install,

even that it reports that all dependencies are correctly installed , dont manage to call Garfield from the path.

i am running R 4.4 so I had to install logicFS via https://www.bioconductor.org/packages/devel/bioc/html/logicFS.html

still sending error below.

do you have a docker container by any chance?

use cpanm at: /usr/local/bin/cpanm

Usage: cpanm [options] Module [...]

Try cpanm --help or man cpanm for more options. sh: 2: --local-lib=~/perl5: not found Perl module Benchmark is already installed. Perl module FindBin is already installed. Perl module File::Spec is already installed. Perl module Pod::Usage is already installed. Perl module Getopt::Long::Subcommand is already installed. Perl module Fcntl is already installed. Perl module Parallel::ForkManager is already installed. Rscript found in the PATH. Installing R libraries 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.0 (2024-04-24) Old packages: 'codetools', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'spatial', 'survival' Warning message: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'logicFS' Required R packages have been successfully installed!

All dependencies have been satisfied. Now you can take Garfield on your journey!

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/_/\ ~ MEOW ~ ( o.o )

^ <

heroalone commented 4 months ago

Hey Miguel, It seems you have installed it successfully and just have no access to run it, since it was not added successfully to the $PATH.

Can you try the absolute path, like: sudo ./Garfield

Or chmod 755 to change the right of the program/folder?

Please let me know if this works and we can continue to the next solution :)