Arch Linux User Repository

The sha256 checksum of the source archive currently doesn't match the PKGBUILD:

9a99fd68ed380894defb4d5e6a8a2871629270028cdf7f16f0a05da6e8c71473 (direct download)

32aa599bc4e8982d173fa638def5a96781322ad53b4ff2013e429a9961cad0e7 (PKGBUILD)

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

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

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

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

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.

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