I am using provean v1.1.5 without the supporting set and it always fails with the following (timestamps removed): [...] retrieving subject sequence information... [...] Parsing Error I have inspected the raw blast_out file and it seems fine: there are lines containing database IDs. Then I looked into the code in src/SequenceDB.cpp, in SequenceDB::SetSequenceInfoFromBlastOut(), and I do not quite get the following line: gi = strtok(NULL, "\t\n"); I may not know C/C++ well, but it seems to me that...
Thanks for the answer, Igor. I now see your point, and it makes much more sense to me.
Sure, this is an option. However, outdated configure.ac might at some point start to hinder the development of the configure script as all modern Autoconfs will refuse reading it. I am aware that configure script does not change much, though.
Yes, the original configure script works. However, Debian package builder attempts to automatically run configure with default Debian options, some of which are not supported by OSRA configure, in particular '--runstatedir=/run'. Rebuilding configure with Autoconf usually makes all such options available. I can in principle strip '--runstatedir=/run' off, but this would be something of a hack in Debian package build.
Autoconf directives need updating
Update: this is possibly caused by URLDecoder.decode(...) used in ClasspathRepository.java, as URL decode perceives '+' in URLs as spaces.
Update: I run into the same issue (failing tests) when I try building jnati in a location where the absolute path contains '+' (say /home/andrius/src/build+jnati/jnati). However, if I replace '+' with '-', I get a successful build.
FileNotFoundException for path with '+'
Thanks for a prompt answer!
Oops, I accidentally posted this in patches. Please transfer to Bugs/Feature requests, where appropriate.
Cannot select atom names with parentheses or quotes
Thanks for the prompt fix! As for 2009633.cif, it seems that the symmetry information...
CIF read crashes when _geom_bond_distance values start with decimal dot
Many thanks for the fix!
Sure, 100.0 was in place only to demonstrate the issue.
Thank you very much for the prompt fix!
Cartesian coordinates are scaled according to the lattice constants in CIF
CIF read crashes with _geom_bond_distance and no lattice constants
I see. Particularly I am interested in reading the bonding details. Here are a few...
I see. Particularly I am interested in reading the bonding details. Here are a few...
Thank you for the prompt reply and incorporation of the patch!
Bond orders are not properly read from _ccdc_geom_bond_type tag (CIF files)