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NKI-CCB / DISCOVER

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
Apache License 2.0
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Installation Fails on Debian 10 #11

Closed DarioS closed 4 years ago

DarioS commented 4 years ago

The software installation worked on Debian 9 last year. The system administrator upgraded the server to Debian 10 during holidays. Now, I can't install DISCOVER.

logspace.f90:12:22:

     real(dp), volatile :: z
                      1
Error: VOLATILE attribute at (1) cannot be specified in a PURE procedure
logspace.f90:14:5:

     z = 1.0d0 + x
     1
Error: Symbol ‘z’ at (1) has no IMPLICIT type
make: *** [/usr/lib/R/etc/Makeconf:195: logspace.o] Error 1
ERROR: compilation failed for package ‘discover’
* removing ‘/dskh/nobackup/biostat/Bioconductor/discover

Can the Fortran code be updated for newer compilers (Fortran is now at version 8.3)? It seems this problem was fixed before #9 but it happens to me today. Perhaps the fix needs to be made to the repository http://ccb.nki.nl/software/discover/repos/r which the installation instructions advise the end-user to set.

scanisius commented 4 years ago

This problem has indeed been fixed in the git repository. Unfortunately, we cannot currently upload new packages to our package repository. We are working to resolve this as soon as possible.

In the meantime, you can install the latest version using the install_github function from the remotes package.

library(remotes)
install_github("NKI-CCB/DISCOVER", subdir="R")
scanisius commented 4 years ago

The latest version of the DISCOVER R package (0.9.3) has now been uploaded to our package repository. So you should be able to follow the original installation instructions again and no longer encounter the compilation error.

DarioS commented 4 years ago

Installation has worked on Debian 10.