PDB-REDO/dssp

dssp-4.4.3: unit-test-dssp.cpp(247): error: in "dssp_3": check f.is_valid() has failed

Closed this issue · 7 comments

pacho2 commented

I get this failure when running tests:

A:130/CYS   E     
A:131/THR   E     
A:132/ARG   E     
A:133/VAL   E     
A:134/TYR   E     
A:135/VAL   E     
A:136/ARG   E     
A:137/GLU         
undefined category dssp_struct_bridge_pairs
undefined category dssp_struct_ladder
undefined category dssp_statistics
undefined category dssp_statistics_hbond
undefined category dssp_statistics_histogram
undefined category dssp_struct_summary
/var/tmp/portage/sci-chemistry/dssp-4.4.3/work/dssp-4.4.3/test/unit-test-dssp.cpp(247): error: in "dssp_3": check f.is_valid() has failed

*** 1 failure is detected in the test module "Master Test Suite"

<end of output>
Test time =   0.23 sec
----------------------------------------------------------
Test Failed.
"unit-test-dssp" end time: Oct 19 17:23 CEST
"unit-test-dssp" time elapsed: 00:00:00
----------------------------------------------------------

End testing: Oct 19 17:23 CEST

Thanks

mhekkel commented

curious. Can you provide some more details? What version? What OS. What version of libcifpp are you using? etc.

pacho2 commented

It is version 4.4.3 and libcifpp-5.2.2. On Gentoo Linux

I have noted that the tests pass fine when dssp is already installed, but fails when it is not

mhekkel commented

Yes, I already expected that, after thinking about this a bit more. It has to do with locating resources required by mkdssp. To work around this, the tests will have to be rewritten to include the resources directory in the source tree.

I'll fix that.

mhekkel commented

Should be fixed in version 4.4.4

pacho2 commented

Thanks

Original error looks to be gone... but now a different error appeared:

Start testing: Oct 20 14:49 CEST
----------------------------------------------------------
1/1 Testing: unit-test-dssp
1/1 Test: unit-test-dssp
Command: "/var/tmp/portage/sci-chemistry/dssp-4.4.4/work/dssp-4.4.4_build/unit-test-dssp" "--" "/var/tmp/portage/sci-chemistry/dssp-4.4.4/work/dssp-4.4.4/test"
Directory: /var/tmp/portage/sci-chemistry/dssp-4.4.4/work/dssp-4.4.4_build
"unit-test-dssp" start time: Oct 20 14:49 CEST
Output:
----------------------------------------------------------
Running 5 test cases...
loading residues
calculating secondary structure
Considering 804 pairs of residues
calculating alpha helices
calculating pp helices
/var/tmp/portage/sci-chemistry/dssp-4.4.4/work/dssp-4.4.4/test/unit-test-dssp.cpp(106): error: in "ut_dssp": check line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0 has failed
mhekkel commented

Ah, that's sad. There were two different version numbers, I need to find out if there is a way to keep a single version for a main and a sub project, without having to update two files.

Version 4.4.4.1 fixes the last issue

pacho2 commented

It works fine

Thanks a lot