Activity for Andrius Merkys
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Andrius Merkys posted a comment on discussion General Discussion
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...
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Thanks for the answer, Igor. I now see your point, and it makes much more sense to me.
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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 However, outdated configure.ac might at some point start to hinder the development of the configure script as all modern Autoconfs will refuse reading it.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.
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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.
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Autoconf directives need updating
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Update: this is possibly caused by URLDecoder.decode(...) used in ClasspathRepository.java, as URL decode perceives '+' in URLs as spaces.
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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.
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FileNotFoundException for path with '+'
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Thanks for a prompt answer!
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Oops, I accidentally posted this in patches. Please transfer to Bugs/Feature requests, where appropriate.
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Cannot select atom names with parentheses or quotes
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Thanks for the prompt fix! As for 2009633.cif, it seems that the symmetry information...
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CIF read crashes when _geom_bond_distance values start with decimal dot
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Many thanks for the fix!
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Sure, 100.0 was in place only to demonstrate the issue.
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Thank you very much for the prompt fix!
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Cartesian coordinates are scaled according to the lattice constants in CIF
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CIF read crashes with _geom_bond_distance and no lattice constants
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I see. Particularly I am interested in reading the bonding details. Here are a few...
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I see. Particularly I am interested in reading the bonding details. Here are a few...
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Thank you for the prompt reply and incorporation of the patch!
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Bond orders are not properly read from _ccdc_geom_bond_type tag (CIF files)
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