Launchpad has imported 13 comments from the remote bug at http://bugzilla.scilab.org/show_bug.cgi?id=15394.
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Read more about Launchpad's inter-bugtracker facilities at https://help.launchpad.net/InterBugTracking. ------------------------------------------------------------------------ On 2018-01-31T09:03:10+00:00 Scilab-a wrote: BUG DESCRIPTION: ---------------- Not able to save or load a variable ERROR LOG: ---------- HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140383204820864: #000: ../../../src/H5G.c line 553 in H5Gget_info(): invalid argument major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140383204820864: #000: ../../../src/H5D.c line 121 in H5Dcreate2(): not a location ID major: Invalid arguments to routine minor: Inappropriate type #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140383204820864: #000: ../../../src/H5F.c line 749 in H5Fclose(): not a file ID major: Invalid arguments to routine minor: Inappropriate type failed to close file HOW TO REPRODUCE THE BUG: ------------------------- - install a brand new debian testing - install scilab 6.0.0 package and dependencies - create any variable (e.g. "stack") - save it with: save("stack.sod","stack") OTHER INFORMATION: ------------------ Scilab also fails to load the ATOMS manager, and it seems to be bound to that problem. Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/0 ------------------------------------------------------------------------ On 2018-08-27T16:41:17+00:00 Sgougeon wrote: *** Bug 15738 has been marked as a duplicate of this bug. *** Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/8 ------------------------------------------------------------------------ On 2018-08-28T14:25:50+00:00 Antoine-monmayrant-scilab wrote: I confirm that this bug is also present under Ubuntu 18.04 64bits. Antoine Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/9 ------------------------------------------------------------------------ On 2018-08-28T15:36:04+00:00 Sgougeon wrote: Antoine, could you please confirm here that this bug is now fixed on the 6.0-branch and on the master one, for this OS, as you did on users@? Thanks Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/10 ------------------------------------------------------------------------ On 2018-08-28T15:39:30+00:00 Sgougeon wrote: PhiRG, Could you please try on Debian with the nightly build: http://www.scilab.org/en/development/nightly_builds/branch60 Thanks Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/11 ------------------------------------------------------------------------ On 2018-08-28T15:45:52+00:00 Antoine-monmayrant-scilab wrote: This bug is resolved scilab-branch-6.0-1534494461 and scilab- master-1534776009, at least for Ubuntu 18.04 64bits. Antoine Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/12 ------------------------------------------------------------------------ On 2018-08-30T09:18:38+00:00 Scilab-a wrote: Hello Samuel, Well done, it works with scilab-branch-6.0-1534494461 now. The atoms manager opens too now. Thank you very much for your work! Philippe Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/13 ------------------------------------------------------------------------ On 2019-04-08T16:55:42+00:00 Stephane-mottelet wrote: There are plenty of users who install distribution packages believing they are "official" packages that still fail with the same problem. We cannot always say them to install the .tar.gz Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/17 ------------------------------------------------------------------------ On 2019-04-08T18:37:59+00:00 Sgougeon wrote: @Stéphane: I don't understand your rationale for reopening this report. Do you mean that there are some distributions packaging the official Scilab 6.0.2, with which the reported problem still occur? Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/18 ------------------------------------------------------------------------ On 2019-04-08T19:02:42+00:00 Stephane-mottelet wrote: Currently, no mainstream dist (Ubuntu, Fedora, ...) packaged Scilab 6.0.2 because the packaged 6.0.1 version does not work already. Just try the following pair of keywords on Google: Scilab Ubuntu Scilab Fedora ... In fact, Scilab 6.0.2 and the master can be built w.r.t hdf5 1.10.n, but at runtime the problem of bug #15394 still occurs. The only version that is supported in Scilab is hdf5 1.8. The problem is that in recent distributions, the matio lib is too recent and absolutely needs hdf5 1.10.n (I have this problem also in OSX when I use brew as a packaging system). The problem is that package maintainers are not informed of this strict dependency :-( Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/19 ------------------------------------------------------------------------ On 2019-04-09T07:41:32+00:00 Clement-david-h wrote: (In reply to Stéphane MOTTELET from comment #9) > Currently, no mainstream dist (Ubuntu, Fedora, ...) packaged Scilab 6.0.2 > because the packaged 6.0.1 version does not work already. Just try the > following pair of keywords on Google: > > Scilab Ubuntu > Scilab Fedora > ... Google is not always up to date :) ; "6.0.1" was mostly reported as buggy due to its startup and search results are also cluttered by it. Scilab 6.0.2 is available as a Fedora package and atomsSystemUpdate works (I just checked) cause Fedora did not update to hdf5 1.10 yet. Mixing packaging issues with upstream bugs seems a bad idea to me, it will make us responsible for packaging Scilab in systems that are free to update/patch/deprecates/etc... If a distribution package wished to upgrade to hdf5 1.10 for some reason, that's ok but when issues arise we could only try to help them fix things on their side and work together to find the root cause (is it hdf5, is it Scilab, is it some obscure compilation mismatch) > In fact, Scilab 6.0.2 and the master can be built w.r.t hdf5 1.10.n, but at > runtime the problem of bug #15394 still occurs. > The only version that is supported in Scilab is hdf5 1.8. The problem is that > in recent distributions, the matio lib is too recent and absolutely > needs hdf5 1.10.n (I have this problem also in OSX when I use brew as a > packaging system). And that's the whole point, hdf5 1.10 seems to have an issue at runtime and matio started to require it. I clarified the summary and let's work on that :) Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/20 ------------------------------------------------------------------------ On 2019-08-06T14:06:15+00:00 N-strelkov wrote: # Intro The text below is not related to official binary builds of Scilab (6.0.2 and latest from https://build.scilab.org/view/Scilab%20master/job/scilab-master-linux-64/ ). They are not affected by the problem as they continue to use HDF 1.8.14 (see `lib/thirdparty/libhdf5.settings` for confirmation). # Problem The rpm- and deb- packages in GNU/Linux distributions have broken `save` and `load` functionality. Currently many Linux distributions switched to HDF 1.10.x branch: | Distibution | Scilab | HDF5 | `save`/ `load` | | ------------------- | ------ | ------ | ------------------------ | | Debian 10 Buster | 6.0.1 | 1.10.4 | !!! bug !!! | | Ubuntu 18.04 LTS | 6.0.1 | 1.10.0 | !!! bug !!! (LP#1765503) | | Ubuntu 19.04 | 6.0.2 | 1.10.4 | !!! bug !!! (LP#1765503) | | Fedora RawHide | 6.0.2 | 1.10.5 | !!! bug !!! | | Mageia 7 | 6.0.2 | 1.10.5 | !!! bug !!! | | OpenSuSe Leap 15.1 | 6.0.2 | 1.10.4 | !!! bug !!! | | OpenSuSe Tumbleweed | 6.0.2 | 1.10.4 | !!! bug !!! | You can see Scilab packaged version in distributions on Repology - https://repology.org/project/scilab/packages . Below is a text output of `test_run('hdf5')` from Ubuntu 18.04.2 LTS without Details section as example: ``` --> test_run('hdf5') TMPDIR = /tmp/SCI_TMP_213_5dIgF3 Module 001/001 - [hdf5] : 001/046 - [hdf5] binary_bit-for-bit..........................failed: Slave Scilab exited with error code 1 002/046 - [hdf5] h5attr......................................failed: Slave Scilab exited with error code 1 003/046 - [hdf5] h5close.....................................failed: Slave Scilab exited with error code 1 004/046 - [hdf5] h5cp........................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 005/046 - [hdf5] h5dataset...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 006/046 - [hdf5] h5exists....................................failed: Slave Scilab exited with error code 1 007/046 - [hdf5] h5flush.....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 008/046 - [hdf5] h5group.....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 009/046 - [hdf5] h5isAttr....................................failed: Slave Scilab exited with error code 1 010/046 - [hdf5] h5isFile....................................failed: Slave Scilab exited with error code 1 011/046 - [hdf5] h5isGroup...................................failed: Slave Scilab exited with error code 1 012/046 - [hdf5] h5isRef.....................................failed: Slave Scilab exited with error code 1 013/046 - [hdf5] h5isSet.....................................failed: Slave Scilab exited with error code 1 014/046 - [hdf5] h5isSpace...................................failed: Slave Scilab exited with error code 1 015/046 - [hdf5] h5isType....................................failed: Slave Scilab exited with error code 1 016/046 - [hdf5] h5label.....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 017/046 - [hdf5] h5ln........................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 018/046 - [hdf5] h5ls........................................failed: Slave Scilab exited with error code 1 019/046 - [hdf5] h5mount.....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 020/046 - [hdf5] h5mv........................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 021/046 - [hdf5] h5open......................................failed: Slave Scilab exited with error code 1 022/046 - [hdf5] h5read......................................failed: Slave Scilab exited with error code 1 023/046 - [hdf5] h5readattr..................................failed: Slave Scilab exited with error code 1 024/046 - [hdf5] h5rm........................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 025/046 - [hdf5] h5umount....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 026/046 - [hdf5] h5write.....................................failed: Slave Scilab exited with error code 1 027/046 - [hdf5] loadhdf5data................................failed: Slave Scilab exited with error code 1 028/046 - [hdf5] loadhdf5data_v1.............................failed: Slave Scilab exited with error code 1 029/046 - [hdf5] saveloadHdf5................................failed: Slave Scilab exited with error code 1 030/046 - [hdf5] bug_11954...................................failed: Slave Scilab exited with error code 1 031/046 - [hdf5] bug_12285...................................failed: Slave Scilab exited with error code 1 032/046 - [hdf5] bug_13689...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 033/046 - [hdf5] bug_13941...................................failed: Slave Scilab exited with error code 1 034/046 - [hdf5] bug_14149...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 035/046 - [hdf5] bug_14446...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 036/046 - [hdf5] bug_14775...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 037/046 - [hdf5] bug_14886...................................failed: Slave Scilab exited with error code 1 038/046 - [hdf5] bug_15188...................................failed: Slave Scilab exited with error code 1 039/046 - [hdf5] bug_15302...................................failed: Slave Scilab exited with error code 1 040/046 - [hdf5] bug_5629....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 041/046 - [hdf5] bug_6440....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 042/046 - [hdf5] bug_7224....................................failed: Slave Scilab exited with error code 1 043/046 - [hdf5] bug_8170....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 044/046 - [hdf5] bug_8383....................................failed: Slave Scilab exited with error code 1 045/046 - [hdf5] bug_9510....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 046/046 - [hdf5] matrix_as_input.............................failed: error_output not empty Use 'no_check_error_output' option to disable this check. -------------------------------------------------------------------------- Summary tests 46 - 100 % passed 0 - 0 % failed 46 - 100 % skipped 0 length 14.40 sec -------------------------------------------------------------------------- ... ``` You can see how worse is the situation. The simple test with *loading* of existing file with variables produces the output below: ``` --> unix('file x.dat'); x.dat: Hierarchical Data Format (version 5) data --> load('x.dat') HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140409678010240: #000: ../../../src/H5F.c line 749 in H5Fclose(): not a file ID major: Invalid arguments to routine minor: Inappropriate type failed to close fileHDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140409678010240: #000: ../../../src/H5G.c line 553 in H5Gget_info(): invalid argument major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140409678010240: #000: ../../../src/H5F.c line 749 in H5Fclose(): not a file ID major: Invalid arguments to routine minor: Inappropriate type failed to close file --> ``` The simple test with *saving* file with variables produces the output below: ``` --> y=100; --> save('y.dat','y') HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140409678010240: #000: ../../../src/H5G.c line 553 in H5Gget_info(): invalid argument major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140409678010240: #000: ../../../src/H5D.c line 121 in H5Dcreate2(): not a location ID major: Invalid arguments to routine minor: Inappropriate type #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140409678010240: #000: ../../../src/H5F.c line 749 in H5Fclose(): not a file ID major: Invalid arguments to routine minor: Inappropriate type failed to close file save: Unable to export variable 'y' in file 'y.dat'. ``` And as a side-effect we can see that `atomsSystemUpdate()` is broken too (really caused by broken `save()`): ``` --> atomsSystemUpdate Scanning repository http://atoms.scilab.org/6.0 ... Done HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140626028816256: #000: ../../../src/H5G.c line 553 in H5Gget_info(): invalid argument major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140626028816256: #000: ../../../src/H5G.c line 301 in H5Gcreate2(): not a location major: Invalid arguments to routine minor: Inappropriate type #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140626028816256: #000: ../../../src/H5A.c line 265 in H5Acreate2(): not a location major: Invalid arguments to routine minor: Inappropriate type #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140626028816256: #000: ../../../src/H5D.c line 121 in H5Dcreate2(): not a location ID major: Invalid arguments to routine minor: Inappropriate type #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140626028816256: #000: ../../../src/H5F.c line 749 in H5Fclose(): not a file ID major: Invalid arguments to routine minor: Inappropriate type failed to close fileat line 265 of function atomsDESCRIPTIONget ( /usr/share/scilab/modules/atoms/macros/atoms_internals/atomsDESCRIPTIONget.sci line 284 ) at line 16 of function atomsSystemUpdate ( /usr/share/scilab/modules/atoms/macros/atomsSystemUpdate.sci line 33 ) atomsDESCRIPTIONget: save ('/usr/share/scilab//.atoms/packages') has failed. --> ``` # Brief analysis I believe that root cause of the problem is change of `hid_t` datatype in HDF library. It is not an `int` anymore, it is `int64_t`. But the scilab source code have many places with hardcoded `int`. See for example `openHDF5File` - http://cgit.scilab.org/scilab/tree/scilab/modules/hdf5/src/c/h5_fileManagement.c which calls `H5Fopen`: ``` int openHDF5File(const char *name, int _iAppendMode) { hid_t file; ... file = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT); ... return file; } ``` that is incorrect truncation of long integer. The same is related to Datasets and Groups - they are also `hid_t` (not `int`). # Conclusion I tried to patch this way locally, but it is difficult. I do not understand the whole `module/hdf5` structure. So I do not get success. Please take this comment into account seriously. Other users and I can't imagine Scilab usage without `save`, `load` and ATOMS... Using deb- and rpm-packages is more convenient than binary distribution, so bug should be fixed with joint efforts of Scilab Team (upstream for distributions) and maintainers. Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/34 ------------------------------------------------------------------------ On 2019-08-07T22:54:25+00:00 N-strelkov wrote: Created attachment 4992 Patches for Ubuntu (18.04 LTS and 19.04) and master branch # Intro I have analyzed the source code of the `modules/hdf5` folder. I have used KDevelop IDE for doing so. It has full feature *Semantic code* analyzer ( https://www.kdevelop.org/screenshots/c-semantic-information-tooltip ). Without KDevelop you can detect problems with datatypes after adding `-Wconversion` to the CFGLAGS and CXXFLAGS variables inside `modules/hdf5/Makefile`. Usually the warning messages from GCC look like: ``` src/c/h5_writeDataToFile.c: In function 'writeStringMatrix': src/c/h5_writeDataToFile.c:296:27: warning: conversion to 'int' from 'hid_t {aka long int}' may alter its value [-Wconversion] status = addAttribute(dset, g_SCILAB_CLASS, g_SCILAB_CLASS_STRING); ^~~~ ... src/c/h5_fileManagement.c: In function 'openHDF5File': src/c/h5_fileManagement.c:161:12: warning: conversion to 'int' from 'hid_t {aka long int}' may alter its value [-Wconversion] return file; ^~~~ ... src/c/h5_fileManagement.c: In function 'createHDF5File': src/c/h5_fileManagement.c:101:12: warning: conversion to 'int' from 'hid_t {aka long int}' may alter its value [-Wconversion] return file; ^~~~ sci_gateway/cpp/sci_hdf5_listvar_v3.cpp: In function 'bool read_struct(int, VarInfo6&)': sci_gateway/cpp/sci_hdf5_listvar_v3.cpp:738:42: warning: conversion to 'int' from 'hid_t {aka long int}' may alter its value [-Wconversion] int data = H5Rdereference(refs, ``` and so on. # Patching I attach 3 patches to fix HDF-related problems in Ubuntu (18.04 LTS and 19.04) and in master branch. ## Ubuntu 18.04 LTS Applying patch is as follows: ``` sudo apt-get build-dep scilab cd ~/Downloads apt-get source scilab cd scilab-6.0.1 dpkg-builpackage -b -j$(nproc) # build to see current state cd modules/hdf5 patch -p1 < ~/Downloads/scilab-6.0.1-ubuntu-bionic.patch cd ../.. dpkg-builpackage -b -j$(nproc) # build to see changes ``` As the patch is applied then we can test patched Scilab. The results from `test_run('hdf5')` are the following: ``` -->test_run('hdf5') TMPDIR = /tmp/SCI_TMP_2556_AWXxWF Module 001/001 - [hdf5] : 001/046 - [hdf5] binary_bit-for-bit..........................passed 002/046 - [hdf5] h5attr......................................passed 003/046 - [hdf5] h5close.....................................passed 004/046 - [hdf5] h5cp........................................passed 005/046 - [hdf5] h5dataset...................................passed 006/046 - [hdf5] h5exists....................................passed 007/046 - [hdf5] h5flush.....................................passed 008/046 - [hdf5] h5group.....................................passed 009/046 - [hdf5] h5isAttr....................................passed 010/046 - [hdf5] h5isFile....................................passed 011/046 - [hdf5] h5isGroup...................................passed 012/046 - [hdf5] h5isRef.....................................passed 013/046 - [hdf5] h5isSet.....................................passed 014/046 - [hdf5] h5isSpace...................................passed 015/046 - [hdf5] h5isType....................................passed 016/046 - [hdf5] h5label.....................................passed 017/046 - [hdf5] h5ln........................................passed 018/046 - [hdf5] h5ls........................................passed 019/046 - [hdf5] h5mount.....................................passed 020/046 - [hdf5] h5mv........................................passed 021/046 - [hdf5] h5open......................................passed 022/046 - [hdf5] h5read......................................passed 023/046 - [hdf5] h5readattr..................................passed 024/046 - [hdf5] h5rm........................................passed 025/046 - [hdf5] h5umount....................................passed 026/046 - [hdf5] h5write.....................................passed 027/046 - [hdf5] loadhdf5data................................passed 028/046 - [hdf5] loadhdf5data_v1.............................passed 029/046 - [hdf5] saveloadHdf5................................passed 030/046 - [hdf5] bug_11954...................................passed 031/046 - [hdf5] bug_12285...................................passed 032/046 - [hdf5] bug_13689...................................passed 033/046 - [hdf5] bug_13941...................................passed 034/046 - [hdf5] bug_14149...................................passed 035/046 - [hdf5] bug_14446...................................passed 036/046 - [hdf5] bug_14775...................................passed 037/046 - [hdf5] bug_14886...................................failed: Slave Scilab exited with error code 51 038/046 - [hdf5] bug_15188...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 039/046 - [hdf5] bug_15302...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 040/046 - [hdf5] bug_5629....................................passed 041/046 - [hdf5] bug_6440....................................passed 042/046 - [hdf5] bug_7224....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 043/046 - [hdf5] bug_8170....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 044/046 - [hdf5] bug_8383....................................passed 045/046 - [hdf5] bug_9510....................................passed 046/046 - [hdf5] matrix_as_input.............................passed -------------------------------------------------------------------------- Summary tests 46 - 100 % passed 41 - 89 % failed 5 - 10 % skipped 0 length 22.47 sec -------------------------------------------------------------------------- ``` Note: in output above cases with `error_output not empty` are not critical, the output really contain warnings on Scilab start, so all asserts were satisfied. The ATOMS works - tested `atomsSystemUpdate`, `atomsShow` and `atomsInstall`. ## Ubuntu 19.04 Applying patch is as follows: ``` sudo apt-get build-dep scilab cd ~/Downloads apt-get source scilab cd scilab-6.0.2 dpkg-builpackage -b -j$(nproc) # build to see current state cd modules/hdf5 patch -p1 < ~/Downloads/scilab-6.0.2-ubuntu-disco.patch cd ../.. dpkg-builpackage -b -j$(nproc) # build to see changes ``` As the patch is applied then we can test patched Scilab. The results from `test_run('hdf5')` are the following: ``` -->test_run('hdf5') TMPDIR = /tmp/SCI_TMP_6072_vVoEAx Module 001/001 - [hdf5] : 001/052 - [hdf5] binary_bit-for-bit..........................passed 002/052 - [hdf5] h5attr......................................passed 003/052 - [hdf5] h5close.....................................passed 004/052 - [hdf5] h5cp........................................passed 005/052 - [hdf5] h5dataset...................................failed: Slave Scilab exited with error code 1 006/052 - [hdf5] h5exists....................................passed 007/052 - [hdf5] h5flush.....................................passed 008/052 - [hdf5] h5group.....................................passed 009/052 - [hdf5] h5isAttr....................................passed 010/052 - [hdf5] h5isFile....................................passed 011/052 - [hdf5] h5isGroup...................................passed 012/052 - [hdf5] h5isRef.....................................passed 013/052 - [hdf5] h5isSet.....................................passed 014/052 - [hdf5] h5isSpace...................................passed 015/052 - [hdf5] h5isType....................................passed 016/052 - [hdf5] h5label.....................................passed 017/052 - [hdf5] h5ln........................................passed 018/052 - [hdf5] h5ls........................................passed 019/052 - [hdf5] h5mount.....................................failed: Slave Scilab exited with error code 1 020/052 - [hdf5] h5mv........................................passed 021/052 - [hdf5] h5open......................................passed 022/052 - [hdf5] h5read......................................passed 023/052 - [hdf5] h5readattr..................................passed 024/052 - [hdf5] h5rm........................................passed 025/052 - [hdf5] h5umount....................................passed 026/052 - [hdf5] h5write.....................................passed 027/052 - [hdf5] loadhdf5data................................passed 028/052 - [hdf5] loadhdf5data_v1.............................passed 029/052 - [hdf5] saveloadHdf5................................passed 030/052 - [hdf5] bug_11954...................................passed 031/052 - [hdf5] bug_12285...................................passed 032/052 - [hdf5] bug_13689...................................passed 033/052 - [hdf5] bug_13941...................................passed 034/052 - [hdf5] bug_14149...................................passed 035/052 - [hdf5] bug_14446...................................passed 036/052 - [hdf5] bug_14775...................................passed 037/052 - [hdf5] bug_14886...................................failed: Slave Scilab exited with error code 51 038/052 - [hdf5] bug_15188...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 039/052 - [hdf5] bug_15302...................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 040/052 - [hdf5] bug_15501...................................passed 041/052 - [hdf5] bug_15502...................................passed 042/052 - [hdf5] bug_15692...................................passed 043/052 - [hdf5] bug_15693...................................passed 044/052 - [hdf5] bug_15721...................................passed 045/052 - [hdf5] bug_15809...................................passed 046/052 - [hdf5] bug_5629....................................passed 047/052 - [hdf5] bug_6440....................................passed 048/052 - [hdf5] bug_7224....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 049/052 - [hdf5] bug_8170....................................failed: error_output not empty Use 'no_check_error_output' option to disable this check. 050/052 - [hdf5] bug_8383....................................passed 051/052 - [hdf5] bug_9510....................................passed 052/052 - [hdf5] matrix_as_input.............................passed -------------------------------------------------------------------------- Summary tests 52 - 100 % passed 45 - 86 % failed 7 - 13 % skipped 0 length 19.30 sec -------------------------------------------------------------------------- ``` Note: in output above cases with `error_output not empty` are not critical, the output really contain warnings on Scilab start, so all asserts were satisfied. The ATOMS works - tested `atomsSystemUpdate`, `atomsShow` and `atomsInstall`. ## Master branch ``` git clone git://git.scilab.org/scilab scilab-master cd scilab-master/scilab patch -p1 -R < ~/Downloads/scilab-master-20190730.patch ``` This patch is untested, please apply it and test by yourself. I was stuck with `./configure` script - it does not find JOGL and Javah. Seems to need patching. # Conclusion Patches provided here should be comprehensively tested. I can't give any warranty about their functionality. But I see that `test_run('hdf5')` have near 100% of passed tests. And ATOMS work as expected after applying these patches. I'm not too familiar with hdf5 integration into Scilab code. I suspect that there maybe problems with figure handles. Many warnings are not fixed for `modules/hdf5/src/cpp/handle_properties.cpp`. For example ``` 860:5: Implicit conversion loses integer precision: 'hid_t' (aka 'long') to 'int' [-Wshorten-64-to-32] ``` but they can't be simply fixed because of deep dependencies from other modules. According to information from HDFGroup - the HDF5 1.8 will be end-of-life very soon ( https://www.hdfgroup.org/2018/06/release-of-hdf5-1-8-21-newsletter-161/ ). So these patches will become actual in very near future after improvement. Reply at: https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1765503/comments/35 ** Changed in: scilab Status: Unknown => Confirmed ** Changed in: scilab Importance: Unknown => High -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1765503 Title: scilab: save, open and ATOMS system is broken in Scilab 6 on bionic, cosmic, disco and eoan To manage notifications about this bug go to: https://bugs.launchpad.net/scilab/+bug/1765503/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
