libcifpp-7.0.4: unit-3d-test / unit-v2-test / model-test fails

[clebreto]

Hi,

Trying to install libcifpp 7.0.4, I stumble across these test failures, and the impossibility to integrate this version of the library into the SBL (https://sbl.inria.fr/).

git clone https://github.com/PDB-REDO/libcifpp.git
cd libcifpp
ccmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local
cmake --build build
cmake --install build
ctest --test-dir build

Internal ctest changing into directory: /pathtolibcifpp/build
Test project /pathtolibcifpp/build
    Start 1: unit-v2-test
1/8 Test #1: unit-v2-test .....................***Failed    0.34 sec
    Start 2: unit-3d-test
2/8 Test #2: unit-3d-test .....................***Failed    0.60 sec
    Start 3: format-test
3/8 Test #3: format-test ......................   Passed    0.17 sec
    Start 4: model-test
4/8 Test #4: model-test .......................***Failed    0.25 sec
    Start 5: rename-compound-test
5/8 Test #5: rename-compound-test .............   Passed    0.24 sec
    Start 6: sugar-test
6/8 Test #6: sugar-test .......................   Passed    1.20 sec
    Start 7: spinner-test
7/8 Test #7: spinner-test .....................   Passed    5.83 sec
    Start 8: validate-pdbx-test
8/8 Test #8: validate-pdbx-test ...............   Passed    0.24 sec

63% tests passed, 3 tests failed out of 8

Total Test time (real) =   8.86 sec

The following tests FAILED:
	  1 - unit-v2-test (Failed)
	  2 - unit-3d-test (Failed)
	  4 - model-test (Failed)
Errors while running CTest
Output from these tests are in: /pathtolibcifpp/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

I attach the log file to the issue.

LastTest.log

The components.cif file is well present in .local/share/libcifpp .

I am running MacOS Sonoma on an arm64 architecture, but the problem might not be constrained to that OS and arch.

[mhekkel]

The trouble is macOS. And I've not yet fixed this. See https://github.com/PDB-REDO/libcifpp/actions

I know, I have to work on this. Trouble is I have no access to a mac so any attempt to work around this is taking a long time.

[clebreto]

I can provide the full log with VERBOSE set to 5 in utilities.cpp. It is 95Mo large, and contains :

DATA "test"
producing data_test
LOOP ""
Tag "_cat_1.id"
producing category cat_1
Tag "_cat_1.id_2"
Value "1"
producing row for category cat_1
producing _cat_1.id -> 1
Value "1"
producing _cat_1.id_2 -> 1
Value "2"
producing row for category cat_1
producing _cat_1.id -> 2
Value "2"
producing _cat_1.id_2 -> 2
Value "3"
producing row for category cat_1
producing _cat_1.id -> 3
Value ""
producing _cat_1.id_2 -> 
LOOP ""
Tag "_cat_2.id"
producing category cat_2
Tag "_cat_2.parent_id"
Tag "_cat_2.parent_id_2"
Value "0"
producing row for category cat_2
producing _cat_2.id -> 0
Value "1"
producing _cat_2.parent_id -> 1
Value "1"
producing _cat_2.parent_id_2 -> 1
Value "1"
producing row for category cat_2
producing _cat_2.id -> 1
Value "1"
producing _cat_2.parent_id -> 1
Value ""
producing _cat_2.parent_id_2 -> 
Value "2"
producing row for category cat_2
producing _cat_2.id -> 2
Value ""
producing _cat_2.parent_id -> 
Value "1"
producing _cat_2.parent_id_2 -> 1
Value "3"
producing row for category cat_2
producing _cat_2.id -> 3
Value ""
producing _cat_2.parent_id -> 
Value ""
producing _cat_2.parent_id_2 -> 
Value "4"
producing row for category cat_2
producing _cat_2.id -> 4
Value "2"
producing _cat_2.parent_id -> 2
Value "2"
producing _cat_2.parent_id_2 -> 2
Value "5"
producing row for category cat_2
producing _cat_2.id -> 5
Value "3"
producing _cat_2.parent_id -> 3
Value "1"
producing _cat_2.parent_id_2 -> 1
Value "6"
producing row for category cat_2
producing _cat_2.id -> 6
Value "3"
producing _cat_2.parent_id -> 3
Value ""
producing _cat_2.parent_id_2 -> 
Eof
warning: no child to parent links were found for child cat_1 and parent cat_3
Error parsing mmCIF: This file does not seem to be an mmCIF file

[mhekkel]

Could you please tell me what version of CLang you're using?

[clebreto]

Hi,

-- The CXX compiler identification is AppleClang 15.0.0.15000100
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- DESTDIR is ''
-- Performing Test GXX_LIBSTDCPP
-- Performing Test GXX_LIBSTDCPP - Failed
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE

[drlemmus]

Could you check the latest release?

[mhekkel]

Proved to be an arm issue, or better, an issue with number formatting when using arm processors.

[clebreto]

Proved to be an arm issue, or better, an issue with number formatting when using arm processors.

Thanks for having looked into it. As soon as I get a moment for testing I'll let you know the status with the latest version.