Package Details: viennarna 2.6.4-3

Git Clone URL: https://aur.archlinux.org/viennarna.git (read-only, click to copy)
Package Base: viennarna
Description: RNA Secondary Structure Prediction and Comparison
Upstream URL: http://www.tbi.univie.ac.at/RNA
Licenses: custom
Groups: viennarna-package
Provides: Kinfold, kinwalker, libRNA, RNAforester, RNAxplorer, viennarna2
Submitter: RaumZeit
Maintainer: RaumZeit
Last Packager: RaumZeit
Votes: 5
Popularity: 0.63
First Submitted: 2015-09-17 22:04 (UTC)
Last Updated: 2024-07-15 07:08 (UTC)

Sources (3)

Latest Comments

olenellus commented on 2024-06-24 15:55 (UTC)

Shouldn't libsvm be included into the (optional) dependencies? The package is build and all the programs work well without it, but it is needed to link libRNA to other programs. See here:

https://bbs.archlinux.org/viewtopic.php?id=296212

tzok commented on 2024-05-06 14:25 (UTC)

The build fails with Python 3.12.3:

RNA_wrap.cpp: In function 'int Swig_var_symbolset_set(PyObject*)':
RNA_wrap.cpp:72354:24: error: 'SWIG_Python_str_AsChar' was not declared in this scope; did you mean 'SWIG_Python_str_FromChar'?
72354 |     symbolset = strdup(SWIG_Python_str_AsChar(_val));
      |                        ^~~~~~~~~~~~~~~~~~~~~~
      |                        SWIG_Python_str_FromChar

RaumZeit commented on 2020-08-04 09:15 (UTC)

The compilation issues have been fixed in release 2 of version 2.4.14

tzok commented on 2020-07-31 10:26 (UTC) (edited on 2020-07-31 10:29 (UTC) by tzok)

The build fails during linking of Kinfold. I am using gcc-10.1.0-2.

  CC       baum.o
  CC       cache.o
  CC       globals.o
  CC       main.o
  CC       nachbar.o
  CC       cmdline.o
  CCLD     Kinfold
/usr/bin/ld: globals.o:(.bss+0x40): multiple definition of `GAV'; baum.o:(.bss+0x40): first defined here
/usr/bin/ld: globals.o:(.bss+0x0): multiple definition of `GTV'; baum.o:(.bss+0x0): first defined here
/usr/bin/ld: globals.o:(.bss+0x8a0): multiple definition of `GSV'; baum.o:(.bss+0x8a0): first defined here
/usr/bin/ld: main.o:(.bss+0x40): multiple definition of `GAV'; baum.o:(.bss+0x40): first defined here
/usr/bin/ld: main.o:(.bss+0x0): multiple definition of `GTV'; baum.o:(.bss+0x0): first defined here
/usr/bin/ld: main.o:(.bss+0x8a0): multiple definition of `GSV'; baum.o:(.bss+0x8a0): first defined here
/usr/bin/ld: nachbar.o:(.bss+0x40): multiple definition of `GAV'; baum.o:(.bss+0x40): first defined here
/usr/bin/ld: nachbar.o:(.bss+0x8a0): multiple definition of `GSV'; baum.o:(.bss+0x8a0): first defined here
/usr/bin/ld: nachbar.o:(.bss+0x0): multiple definition of `GTV'; baum.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status

RaumZeit commented on 2019-05-31 15:28 (UTC)

This problem is due to swig >= 4.0.0. The upstream version has already been adapted to this situation and I've just pushed version 2.4.13 to AUR which fixes this bug.

balwierz commented on 2019-05-15 15:51 (UTC) (edited on 2019-05-15 15:51 (UTC) by balwierz)

Build fails.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/yaourt-tmp-user/aur-perl-rna/src/ViennaRNA-2.4.12/interfaces/Python3/RNA/__init__.py", line 13, in <module>
    from . import _RNA
ImportError: cannot import name '_RNA' from 'RNA' (/tmp/yaourt-tmp-user/aur-perl-rna/src/ViennaRNA-2.4.12/interfaces/Python3/RNA/__init__.py)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/yaourt-tmp-user/aur-perl-rna/src/ViennaRNA-2.4.12/interfaces/Python3/RNA/__init__.py", line 13, in <module>
    from . import _RNA
ImportError: cannot import name '_RNA' from 'RNA' (/tmp/yaourt-tmp-user/aur-perl-rna/src/ViennaRNA-2.4.12/interfaces/Python3/RNA/__init__.py)
make[3]: *** [Makefile:998: RNA/__pycache__/__init__.cpython-37.pyc] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [Makefile:1002: RNA/__pycache__/__init__.cpython-37.opt-1.pyc] Error 1
make[3]: Leaving directory '/tmp/yaourt-tmp-user/aur-perl-rna/src/ViennaRNA-2.4.12/interfaces/Python3'
make[2]: *** [Makefile:606: all-recursive] Error 1
make[2]: Leaving directory '/tmp/yaourt-tmp-user/aur-perl-rna/src/ViennaRNA-2.4.12/interfaces'
make[1]: *** [Makefile:667: all-recursive] Error 1
make[1]: Leaving directory '/tmp/yaourt-tmp-user/aur-perl-rna/src/ViennaRNA-2.4.12'
make: *** [Makefile:560: all] Error 2

RaumZeit commented on 2016-06-30 12:48 (UTC)

This issue is now fixed upstream, since epstopdf is only required for building the reference manual, which, however, is already present in the dist tarball. Now, no rebuild is done and therefore epstopdf is not required anymore.

anntzer commented on 2016-06-26 08:19 (UTC)

This should makedepends on something that provides epstopdf.