** Description changed:
+ [Impact]
+ Scilab 6.0 requires hdf5 1.8 to work, but since Bionic we are shipping HDF5
1.10. This makes hdf5 unusable with Scilab 6.0. Scilab needs to be patched to
work with hdf5 1.10 or updated from 6.0 to 6.1.
+
+ [Test Case]
+ = Expected result =
+
+ $ scilab-cli
+ --> test_run('hdf5')
+ TMPDIR = /tmp/SCI_TMP_10959_EouWeO
+
+ 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...................................passed
+ 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.....................................passed
+ 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:
error_output not empty
+ Use
'no_check_error_output' option to disable this check.
+ 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 52 - 100 %
+ failed 0 - 0 %
+ skipped 0
+ length 18.26 sec
+
+ Note: if there's no X11 running or no GL support on X11, then the following 5
tests will fail as in:
+ 037/052 - [hdf5] bug_14886...................................failed:
error_output not empty
+ Use
'no_check_error_output' option to disable this check.
+ 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.
+ 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.
+
+
+ = Current results =
+ All tests fail with "failed: Slave Scilab exited with error code 1".
+
+ $ scilab-cli
+ --> test_run('hdf5')
+ (snip)
+ Summary
+
+ tests 52 - 100 %
+ passed 0 - 0 %
+ failed 52 - 100 %
+ skipped 0
+ length 11.22 sec
+
+
+ [Regression Potential]
+ * The patch for hdf5 1.10 basically changes the type of a variable from int
to hid_t, it does not change any logic in the code. As all hdf5 calls that rely
in that variable currently fail and this change is limited to hdf5, no
regressions are actually expected.
+
+ [Other Info]
+ * Scilab 6.1 does support hdf5 1.10 and is available on Focal, but cannot be
backported to Bionic as it depends on std::filesystem::weakly_canonical which
is available on Bionic only in g++-8 - and std::experimental::filesystem from
g++-7 does not implement/exports weakly_canonical.
+ * The original report references to atomsShow('coselica'), but that
reproducer can only be used on scilab 6.0 as coselica does not support scilab
6.1. Thus it is better to rely on the generic test_run('hdf5').
+
+
+ [Original report]
+
Steps to reproduce:
1. Install Ubuntu 18.04 LTS (x86_64 in my case)
2. Install `scilab` package
3. Launch Scilab CLI (as normal `scilab` does not start because of bug
1762999) from terminal with `scilab-cli`
4. Try to show information of a package from ATOMS system with
`atomsShow('coselica')`
Expected results:
* Scilab updates local ATOMS cache, then shows information about Coselica
toolbox
Actual results:
* Scilab shows error in its console:
--> atomsShow('coselica')
Scanning repository http://atoms.scilab.org/6.0 ... Done
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140526662825856:
- #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 140526662825856:
- #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 140526662825856:
- #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 140526662825856:
- #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 140526662825856:
- #000: ../../../src/H5F.c line 749 in H5Fclose(): not a file ID
- major: Invalid arguments to routine
- minor: Inappropriate type
+ #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 140526662825856:
+ #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 140526662825856:
+ #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 140526662825856:
+ #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 140526662825856:
+ #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 31 of function atomsIsPackage (
/usr/share/scilab/modules/atoms/macros/atoms_internals/atomsIsPackage.sci line
47 )
at line 43 of function atomsShow (
/usr/share/scilab/modules/atoms/macros/atomsShow.sci line 59 )
atomsDESCRIPTIONget: save
('/home/beaver/.Scilab/scilab-6.0.1/.atoms/packages') has failed.
ProblemType: Bug
DistroRelease: Ubuntu 18.04
Package: scilab-cli 6.0.1-1ubuntu1
ProcVersionSignature: Ubuntu 4.15.0-17.18-generic 4.15.17
Uname: Linux 4.15.0-17-generic x86_64
ApportVersion: 2.20.9-0ubuntu5
Architecture: amd64
CurrentDesktop: MATE
Date: Thu Apr 19 22:08:58 2018
PackageArchitecture: all
SourcePackage: scilab
UpgradeStatus: No upgrade log present (probably fresh install)
- ---
+ ---
ProblemType: Bug
ApportVersion: 2.20.9-0ubuntu7.6
Architecture: amd64
CurrentDesktop: MATE
DistroRelease: Ubuntu 18.04
InstallationDate: Installed on 2018-04-26 (354 days ago)
InstallationMedia: Ubuntu-MATE 18.04 LTS "Bionic Beaver" - Release amd64
(20180426)
Package: scilab 6.0.1-7ubuntu1~18.04
PackageArchitecture: all
ProcVersionSignature: Ubuntu 4.15.0-47.50-generic 4.15.18
Tags: bionic
Uname: Linux 4.15.0-47-generic x86_64
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin plugdev sambashare sudo
_MarkForUpload: True
- ---
+ ---
ProblemType: Bug
ApportVersion: 2.20.10-0ubuntu13.2
Architecture: amd64
CurrentDesktop: MATE
DistroRelease: Ubuntu 18.10
InstallationDate: Installed on 2019-02-17 (58 days ago)
InstallationMedia: Ubuntu-MATE 18.10 "Cosmic Cuttlefish" - Release amd64
(20181017.2)
Package: scilab 6.0.1-7ubuntu1~18.10
PackageArchitecture: all
ProcVersionSignature: Ubuntu 4.18.0-16.17-generic 4.18.20
Tags: cosmic
Uname: Linux 4.18.0-16-generic x86_64
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm cdrom dip lpadmin plugdev sambashare sudo
_MarkForUpload: True
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https://bugs.launchpad.net/bugs/1765503
Title:
scilab: hdf5 is broken in Scilab 6.0 on bionic
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