Bug#1090900: fenics-dolfinx: autopkgtest regressions with HDF5 1.14

2024-12-20 Thread Gilles Filippini
Source: fenics-dolfinx Version: 1:0.9.0-5 Severity: serious -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Control: user p...@debian.org Control: usertags + hdf5-1.14 Hi, Since the upload of hdf5 1.14.5 to unstable the autopkgtest of fenics-dolfinx have regressed on all architectures. See for

Bug#1090899: fclib: autopkgtest regressions with HDF5 1.14

2024-12-20 Thread Gilles Filippini
Source: fclib Version: 3.1.0+dfsg-3 Severity: serious -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Control: user p...@debian.org Control: usertags + hdf5-1.14 Hi, Since the upload of hdf5 1.14.5 to unstable the autopkgtest of fclib have regressed on all architectures. See for instance: http

Bug#1090898: fast5: autopkgtest regressions with HDF5 1.14

2024-12-20 Thread Gilles Filippini
Source: fast5 Version: 0.6.5-8 Severity: serious -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Control: user p...@debian.org Control: usertags + hdf5-1.14 Hi, Since the upload of hdf5 1.14.5 to unstable the autopkgtest of fast5 have regressed on all architectures. See for instance: https://c

Bug#1089016: Depends: r-api-bioc-3.20 but it is not installable

2024-12-04 Thread Gilles Filippini
Package: r-bioc-biocstyle Version: 2.34.0+dfsg-1 Severity: serious Justification: uninstallable -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, r-bioc-biocstyle in unstable is currently uninstallable: (unstable-amd64-sbuild)root:~# apt install r-bioc-biocstyle Some packages could not be ins

Bug#1088789: adios2: FTBFS with HDF5 1.14: dh_missing: warning: usr/lib/x86_64-linux-gnu/libadios2_h5vol.so exists in install-serial but is not installed to anywhere

2024-12-01 Thread Gilles Filippini
:25.0 +0100 +++ adios2-2.10.1+dfsg1/debian/changelog2024-12-01 14:36:06.0 +0100 @@ -1,3 +1,10 @@ +adios2 (2.10.1+dfsg1-13.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Disable HDF5_VOL to workaround FTBFS with HDF5 1.14 + + -- Gilles Filippini Sun, 01

Bug#1088632: transition: hdf5

2024-11-28 Thread Gilles Filippini
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi Release Team, I am requesting a transition slot for HDF5 1.14 currently in experimental. I've run a test rebuild of the 154 reverse d

Bug#1087826: r-bioc-rhdf5: FTBFS with HDF5 1.14: ‘H5I_REFERENCE’ undeclared (first use in this function)

2024-11-19 Thread Gilles Filippini
0 +0100 @@ -1,3 +1,10 @@ +r-bioc-rhdf5 (2.48.0+dfsg-3.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Support HDF5 1.14 + + -- Gilles Filippini Mon, 18 Nov 2024 12:26:57 +0100 + r-bioc-rhdf5 (2.48.0+dfsg-3) unstable; urgency=medium * Team upload. diff -Nru r-bioc-rhdf5-2.4

Bug#1087772: grads: FTBFS with HDF5 1.14: too few arguments to function ‘H5Oget_info3’

2024-11-18 Thread Gilles Filippini
2.1-8.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Add -DH5_USE_110_API to CFLAGS to fix FTBFS against HDF5-1.14 + + -- Gilles Filippini Sun, 17 Nov 2024 21:43:25 +0100 + grads (3:2.2.1-8) unstable; urgency=medium * Temporarily drop libsx support. Closes: #1080994 diff -Nru grad

Bug#1087776: ncl: FTBFS with HDF5 1.14: too few arguments to function ‘H5Oget_info_by_name3’

2024-11-18 Thread Gilles Filippini
; PREEMPT) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled -BEGIN PGP SIGNATURE- iQEzBAEBCgAdFiEE

Bug#1087764: FTBFS: /usr/bin/ld: unrecognized option '-Wl'

2024-11-18 Thread Gilles Filippini
Source: paraview Version: 5.13.1+dfsg-8 Severity: serious Tags: ftbfs Justification: FTBFS -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, During a test rebuild paraview FTBFS on unstable amd64 with this error: [ 0%] Linking C shared library ../../../lib/x86_64-linux-gnu/libvtkWrappingToo

Bug#1087738: hkl: FTBFS against HDF5 1.14: Module ‘Bindings.HDF5.Raw’ does not export ‘H5L_info_t’

2024-11-17 Thread Gilles Filippini
Source: hkl Version: 5.1.2-2 Severity: important Tags: ftbfs -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The khl package fails to build from source in a test rebuild against hdf5 1.14.5 currentyl in experimental: [18 of 35] Compiling Hkl.H5 ( src/Hkl/H5.hs, /build/hkl-v9xamY/

Bug#1086209: mpif90.openmpi: Cannot open module file 'mpi.mod' for reading at (1): No such file or directory

2024-10-28 Thread Gilles Filippini
Package: openmpi-bin Version: 5.0.5-4 Severity: serious Tags: ftbfs Control: affects -1 src:hdf5 -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, mpif90 fails to build a simple executable on any arch other then amd64. For instance on arm64: $ cat toto.f90 PROGRAM FC_MPI_CHECK USE mpi I

Bug#1078987: cbflib: FTBFS against HDF5 1.14 - Needs -DH5_USE_110_API

2024-08-18 Thread Gilles Filippini
Source: cbflib Version: 0.9.7+dfsg1-3.1 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The cbflib package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=.

Bug#1078984: csound-plugins: FTBFS against HDF5 1.14 - Needs -DH5_USE_110_API

2024-08-18 Thread Gilles Filippini
Source: csound-plugins Version: 1.0.2~dfsg1-3 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The csound-plugins package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: cd "/<>/obj-x86_64-linux-gnu/hdf5" && /usr/bin/cc -DHAVE_SOC

Bug#1078982: uncalled: FTBFS against HDF5 1.14 - Needs -DH5_USE_110_API

2024-08-18 Thread Gilles Filippini
Source: uncalled Version: 2.3+ds-1 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The uncalled package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wal

Bug#1078976: fast5: FTBFS against HDF5 1.14 - Needs -DH5_USE_110_API

2024-08-18 Thread Gilles Filippini
Source: fast5 Version: 0.6.5-7 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The fast5 package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -

Bug#1078975: field3d: FTBFS against HDF5 1.14 - Needs -DH5_USE_110_API

2024-08-18 Thread Gilles Filippini
Source: field3d Version: 1.7.3-4.1 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The field3d package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: /<>/src/Field3DFileHDF5.cpp: In function ‘herr_t Field3D::v1_7::InputFileHDF5

Bug#1078968: libsis-jhdf5-java: FTBFS against HDF5 1.14

2024-08-18 Thread Gilles Filippini
Source: libsis-jhdf5-java Version: 19.04.1+dfsg-6 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The libsis-jhdf5-java package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental. Full build log attached, although I fail to see any re

Bug#1078921: r-cran-hdf5r: FTBFS against HDF5 1.14

2024-08-17 Thread Gilles Filippini
Source: r-cran-hdf5r Version: 1.3.9+dfsg-1 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The r-cran-hdf5r package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/hdf5/serial

Bug#1078904: silo-llnl: FTBFS against HDF5 1.14

2024-08-17 Thread Gilles Filippini
Source: silo-llnl Version: 4.11-6 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The silo-llnl package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I../.. -I./../silo -I./../silo

Bug#1078882: sra-sdk: FTBFS against HDF5 1.14

2024-08-17 Thread Gilles Filippini
Source: sra-sdk Version: 3.0.3+dfsg-8 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The sra-sdk package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: cd /<>/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLIN

Bug#1078860: unifrac-tools: FTBFS against HDF5 1.14

2024-08-17 Thread Gilles Filippini
Source: unifrac-tools Version: 1.4-3 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The unifrac-tools package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental. The failure occurs during the post-build tests. Here is the related ex

Bug#1078824: grads: FTBFS against HDF5 1.14

2024-08-16 Thread Gilles Filippini
Source: grads Version: 3:2.2.1-6 Severity: important -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The grads package fails to build from source in a test rebuild against hdf5 1.14 currently in experimental: gaio.c: In function ‘h5pattrs’: /usr/include/hdf5/serial/H5version.h:921:23: error

Bug#1067950: hdf5: diff for NMU version 1.10.10+repack-3.3

2024-03-29 Thread Gilles Filippini
Andrey Rakhmatullin a écrit le 29/03/2024 à 12:26 : Package: hdf5 Version: 1.10.10+repack-3.2 Severity: normal Tags: patch pending Dear maintainer, I've prepared an NMU for hdf5 (versioned as 1.10.10+repack-3.3) and uploaded it to DELAYED/3. Please feel free to tell me if I should delay it lon

Bug#1067118: nmu: hdf5_1.10.10+repack-3.1

2024-03-18 Thread Gilles Filippini
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: binnmu -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, During the ongoing 64 bit time_t transition it seems HDF5 should have been triggered *after* curl. See #1065331. As I understand it this

Bug#1065331: libhdf5-103-1t64: depends on libcurl4 instead of libcurl4t64

2024-03-18 Thread Gilles Filippini
Hi Vincent, Vincent Lefevre a écrit le 03/03/2024 à 01:08 : Package: libhdf5-103-1t64 Version: 1.10.10+repack-3.1 Severity: serious libhdf5-103-1t64 depends on libcurl4 instead of libcurl4t64. This makes the upgrade of curl impossible. How am I expected to solve this issue? As I understand it

Bug#1064095: hdf5: NMU diff for 64-bit time_t transition

2024-03-18 Thread Gilles Filippini
Hi Steve, Steve Langasek a écrit le 01/03/2024 à 06:06 : Dear maintainer, Please find attached a final version of this patch for the time_t transition. This patch is being uploaded to unstable. Note that this adds a versioned build-dependency on dpkg-dev, to guard against accidental backports

Bug#1050952: r-bioc-rhdf5lib: autopkgtest regression: Expected '1.10.8', got '1.10.10'

2023-08-31 Thread Gilles Filippini
Source: r-bioc-rhdf5lib Version: 1.6.3+dfsg-1 Severity: serious Justification: Test regression -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, See https://ci.debian.net/data/autopkgtest/unstable/amd64/r/r-bioc-rhdf5lib/37206202/log.gz. > 69s - FAILED[data]: test_library_version.R<3--3>

Bug#1042822: med-fichier: Please upgrade to latest med-fichier version aka 5.0.0

2023-08-31 Thread Gilles Filippini
Christophe Trophime a écrit le 31/08/2023 à 18:57 : - Original Message - From: "Gilles Filippini" To: "Christophe Trophime" , 1042...@bugs.debian.org Sent: Thursday, August 31, 2023 6:47:36 PM Subject: Re: Bug#1042822: med-fichier: Please upgrade to latest med-

Bug#1042822: med-fichier: Please upgrade to latest med-fichier version aka 5.0.0

2023-08-31 Thread Gilles Filippini
Hi Christophe, Christophe Trophime a écrit le 01/08/2023 à 14:35 : Source: med-fichier Version: Please upgrade to 5.0.0 version Severity: normal Dear Maintainer, It would be great if med was upgraded to enable use a Salome 9.11 generated mesh files. Where is it downloadable from? Thx, _g.

Bug#1025492: openjdk-17: Upstream commit f71b21b causes segfault in hdf5 java test suite on arches i386 and mips64el

2022-12-05 Thread Gilles Filippini
On Mon, 05 Dec 2022 20:19:37 +0100 Gilles Filippini wrote: Package: openjdk-17 Version: 17~14-1 Severity: serious Tags: upstream Justification: makes unrelated software on the system break -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, A few weeks ago default-jdk was switched from

Bug#1025492: openjdk-17: Upstream commit f71b21b causes segfault in hdf5 java test suite on arches i386 and mips64el

2022-12-05 Thread Gilles Filippini
Package: openjdk-17 Version: 17~14-1 Severity: serious Tags: upstream Justification: makes unrelated software on the system break -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, A few weeks ago default-jdk was switched from openjdk-11 to openjdk-17. Afterward hdf5 has been suffering FTBFS on

Bug#1025232: hdf5: Build dependencies on openjdk-11 that will not be in bookworm

2022-12-02 Thread Gilles Filippini
Hi, Sebastian Ramacher a écrit le 01/12/2022 à 10:25 : Source: hdf5 Version: 1.10.8+repack-4 Severity: serious Tags: sid bookworm X-Debbugs-Cc: sramac...@debian.org openjdk-11 will not be be part of bookworm (see #1023237). Please adapt the package to use the default JDK version (openjdk-17) in

Bug#1023446: libhdf5-openmpi-dev: h5pcc configured as static build

2022-11-22 Thread Gilles Filippini
Hi Drew, Drew Parsons a écrit le 15/11/2022 à 16:28 : h5py is building fine against the shared libraries with HDF5_USE_SHLIB=yes, but leaves a question about rpath. Notice that `h5pcc --showconfig -shlib` includes "-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi -lhdf5_hl -lhdf5 -Wl,-rpath -Wl,/usr/

Bug#1023446: libhdf5-openmpi-dev: h5pcc configured as static build

2022-11-06 Thread Gilles Filippini
Hi Drew, Drew Parsons a écrit le 04/11/2022 à 11:27 : Package: libhdf5-openmpi-dev Version: 1.10.8+repack-1 Severity: important Control: block 1020054 by -1 h5pcc is showing an unexpected default configuration: $ h5pcc --showconfig gcc -I/usr/include/hdf5/openmpi -L/usr/lib/x86_64-linux-gnu/hd

Bug#1017997: hdf5 ftbfs on s390x

2022-08-23 Thread Gilles Filippini
Hi Steve, Steve Langasek a écrit le 23/08/2022 à 22:40 : Package: hdf5 Version: 1.10.8+repack-1 Severity: serious Tags: patch Justification: ftbfs User: ubuntu-de...@lists.ubuntu.com Usertags: origin-ubuntu kinetic ubuntu-patch Hi Gilles, hdf5 has been failing to build from source on s390x. I

Bug#1011373: jhdf: FTBFS against hdf5 1.12.2 currently in experimental

2022-05-21 Thread Gilles Filippini
Source: jhdf Version: 2.11.0+dfsg-5 Severity: important Tags: ftbfs -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, While rebuilding jhdf against hdf5 1.12.2 in experimental, il failed with: h5Constants.c: In function ‘Java_ncsa_hdf_hdf5lib_HDF5Constants_H5I_1REFERENCE’: h5Constants.c:322:1

Bug#1010202: MatIO test failures against HDF5 1.12.0

2022-05-19 Thread Gilles Filippini
libhdf5 support). Best regards, Thomas Am 19.05.2022 um 10:06 schrieb Sébastien Villemot: Hi Thomas, It turns out that running the testsuite sequentially fixes the problem, as explained by Gilles Filippini (who maintains HDF5 in Debian), see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1010202

Bug#1010202: libmatio: FTBFS against hdf5 1.12.0 currently in experimental - 3 failed tests

2022-05-17 Thread Gilles Filippini
Hi Sébastien, Gilles Filippini a écrit le 02/05/2022 à 11:04 : Hi, Gilles Filippini a écrit le 29/04/2022 à 14:10 : Hi Sébastien, Sébastien Villemot a écrit le 29/04/2022 à 11:45 : Hi Gilles, Le mardi 26 avril 2022 à 10:38 +0200, Gilles Filippini a écrit : Source: libmatio Version: 1.5.23

Bug#1010202: libmatio: FTBFS against hdf5 1.12.0 currently in experimental - 3 failed tests

2022-05-02 Thread Gilles Filippini
Hi, Gilles Filippini a écrit le 29/04/2022 à 14:10 : Hi Sébastien, Sébastien Villemot a écrit le 29/04/2022 à 11:45 : Hi Gilles, Le mardi 26 avril 2022 à 10:38 +0200, Gilles Filippini a écrit : Source: libmatio Version: 1.5.23-1 Severity: important Tags: ftbfs While rebuilding libmatio

Bug#1010202: libmatio: FTBFS against hdf5 1.12.0 currently in experimental - 3 failed tests

2022-04-29 Thread Gilles Filippini
Hi Sébastien, Sébastien Villemot a écrit le 29/04/2022 à 11:45 : Hi Gilles, Le mardi 26 avril 2022 à 10:38 +0200, Gilles Filippini a écrit : Source: libmatio Version: 1.5.23-1 Severity: important Tags: ftbfs While rebuilding libmatio 1.5.23 against hdf5 1.12.0, 3 testcases failed with

Bug#892058: debian-keyring: please automatically send reminder emails to people whose keys will expire soon

2022-04-16 Thread Gilles Filippini
Thanks for the ping! This is very much appreciated. Best, _g.

Bug#998383: nheko: nheko/{armel,armhf} has unsatisfiable dependency

2022-01-02 Thread Gilles Filippini
On Wed, 3 Nov 2021 14:25:41 +0200 Adrian Bunk wrote: Control: reassign -1 src:gst-plugins-good1.0 1.18.5-1 Control: retitle -1 gstreamer1.0-qt5 should again be built on armel/armhf Control: affects -1 nheko On Wed, Nov 03, 2021 at 12:03:20PM +0100, Sebastian Ramacher wrote: > Source: nheko > Ve

Bug#987584: docker.io: docker-proxy does not bind to ipv6 "all network" address

2021-11-08 Thread Gilles Filippini
On Thu, 29 Apr 2021 01:54:56 +0800 Shengjing Zhu wrote: On Mon, Apr 26, 2021 at 1:15 PM Jérémy Viès wrote: > > Package: docker.io > Version: 20.10.5+dfsg1-1+b1 > Severity: important > Tags: ipv6 > > Dear Maintainer, > > >* What led up to the situation? > I'm trying to expose some web app to

Bug#995594: libhdf5[-openmpi]-dev: missing Depends: libcurl-dev

2021-10-12 Thread Gilles Filippini
Drew Parsons a écrit le 04/10/2021 à 21:14 : On 2021-10-03 12:15, Gilles Filippini wrote: Drew Parsons a écrit le 02/10/2021 à 22:17 : ... Since h5pcc and h5cc invoke -lcurl, libhdf5-openmpi-dev, libhdf5-dev (and probably libhdf5-mpich-dev also) should declare Depends: libcurl-dev ... I

Bug#995594: libhdf5[-openmpi]-dev: missing Depends: libcurl-dev

2021-10-03 Thread Gilles Filippini
Hi, Drew Parsons a écrit le 02/10/2021 à 22:17 : Package: libhdf5-openmpi-dev Version: 1.10.7+repack-2 Severity: serious Justification: FTBFS Control: affects -1 src:fenics-dolfinx The hdf5 compiler wrappers declare -lcurl as a linked library e.g. $ h5cc -showconfig | grep curl

Bug#994109: scilab FTBFS with hdf5 1.10.7

2021-09-14 Thread Gilles Filippini
Julien Puydt a écrit le 13/09/2021 à 08:51 : Excellent! Please commit to salsa but don't upload yet Done. Best, _g.

Bug#994109: scilab FTBFS with hdf5 1.10.7

2021-09-12 Thread Gilles Filippini
0 +0200 +++ scilab-6.1.1+dfsg2/debian/changelog 2021-09-12 14:50:46.0 +0200 @@ -1,3 +1,11 @@ +scilab (6.1.1+dfsg2-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * New patch hdf5-1.10.7.patch to disable H5_NO_DEPRECATED_SYMBOLS which +causes FTBFS against HDF5 1.10

Bug#993825: buster-pu: package hdf5/1.10.6+repack-4+deb11u1

2021-09-06 Thread Gilles Filippini
dev dependency to (>= 3.3-3~) (Closes: +#992068) + + -- Gilles Filippini Sun, 15 Aug 2021 15:56:44 +0200 + hdf5 (1.10.6+repack-4) unstable; urgency=medium * Revert support for read-only S3 virtual file driver, as it introduced diff -Nru hdf5-1.10.6+repack/debian/control hdf5-1.10.6+repa

Bug#992068: libhdf5-mpich-dev: please bump libmpich-dev dependency to (>= 3.3-3~)

2021-08-11 Thread Gilles Filippini
Andreas Beckmann a écrit le 10/08/2021 à 17:54 : Package: libhdf5-mpich-dev Version: 1.10.6+repack-4 Severity: serious Tags: patch User: debian...@lists.debian.org Usertags: piuparts During an piuparts upgrade test of libhdf5-mpich-dev on the upgrade path squeeze -> wheezy -> jessie -> stretc

Bug#988722: postgresql-common: Upgrading cluster with postgis does not migrate tables using postgis

2021-06-16 Thread Gilles Filippini
Sebastian Ramacher a écrit le 16/06/2021 à 17:22 : Thanks for uploading the fix! Unfortunately, the changes to the S3 virtual file driver caused regressions in hdf5's reverse dependencies (some of them are caused by missing dependencies for -lcrypto and -lcurl). See https://qa.debian.org/excuses

Bug#988722: postgresql-common: Upgrading cluster with postgis does not migrate tables using postgis

2021-06-14 Thread Gilles Filippini
Hi Andreas, Andreas Beckmann a écrit le 14/06/2021 à 10:18 : On 08/06/2021 13.05, Sebastian Ramacher wrote: Here it is. Now testing upgrades ... There were some new symbols ... but they appeared independently of my changes (I built in bullseye, not sid, in case it does matter). Tests have not

Bug#988722: postgresql-common: Upgrading cluster with postgis does not migrate tables using postgis

2021-06-08 Thread Gilles Filippini
Andreas Beckmann a écrit le 08/06/2021 à 11:57 : On 08/06/2021 08.27, Andreas Beckmann wrote: Or, wait, easier: we can reintroduce metapackages libhdf5*-103 depending on libhdf5*-103-1 and all the other packages containing libraries that were in the merged package in buster. I actually like

Bug#988722: postgresql-common: Upgrading cluster with postgis does not migrate tables using postgis

2021-06-08 Thread Gilles Filippini
Control: reassign -1 postgresql-13-postgis-3 Andreas Beckmann a écrit le 08/06/2021 à 08:27 : An alternative solution would be to rename libhdf5*-103-1 back to libhdf5*-103 and add dependencies on the split out libraries (s.t. e.g. dependencies of a buster package depending on libhdf5-103 for a

Bug#988722: postgresql-common: Upgrading cluster with postgis does not migrate tables using postgis

2021-06-07 Thread Gilles Filippini
Hi, On Wed, 2 Jun 2021 22:22:04 +0200 Sebastian Ramacher wrote: Hi Gilles, hi Andreas, On 2021-06-01 14:15:52 +0200, Andreas Beckmann wrote: > On Tue, 18 May 2021 20:36:23 +0200 Dennis Filder wrote: > > One more observation: Bullseye's gdal-data 3.2.1+dfsg-1 defines a > > Breaks: libgdal20 (

Bug#968559: libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing

2020-11-08 Thread Gilles Filippini
Drew Parsons a écrit le 08/11/2020 à 05:17 : > Probably we should check with the update-alternatives developers first, > they may have some ideas. Certainly they should be able to explain > exactly why installing openmpi-bin or mpich causes the hdf5-mpi > alternative to disappear. Would you mind o

Bug#968559: libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing

2020-11-07 Thread Gilles Filippini
Gilles Filippini a écrit le 07/11/2020 à 19:36 : > Drew Parsons a écrit le 06/11/2020 à 04:02 : >> On 2020-11-06 02:09, Gilles Filippini wrote: >>>> >>>> But we should document (or fix if possible) that this alternatives >>>> mechanism is a littl

Bug#968559: libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing

2020-11-07 Thread Gilles Filippini
Drew Parsons a écrit le 06/11/2020 à 04:02 : > On 2020-11-06 02:09, Gilles Filippini wrote: >>> >>> But we should document (or fix if possible) that this alternatives >>> mechanism is a little fragile, and sometimes the link needs to be >>> refresh with >

Bug#968559: libhdf5-openmpi-dev: hdf5-mpi.pc alternative sometimes goes missing

2020-11-05 Thread Gilles Filippini
Control: tag -1 moreinfo Hi Drew, On Mon, 17 Aug 2020 19:23:05 +0800 Drew Parsons wrote: > Package: libhdf5-openmpi-dev > Version: 1.10.6+repack-2 > Severity: normal > > We've set up libhdf5-openmpi-dev (and libhdf5-mpich-dev) to use the > alternatives mechanism to configure a symlink f

Bug#958174: hdf5: please add the hdf5plugins

2020-11-02 Thread Gilles Filippini
Gilles Filippini a écrit le 24/04/2020 à 10:03 : > picca a écrit le 22/04/2020 à 16:07 : >> I found also this link with all the filter available around hdf5. >> so I tought that the hdfgroup would provide a tar.gz with all of them >> pre packaged in source forme. >> &g

Bug#973261: libhdf5-openmpi-dev: installing requires /proc being mounted

2020-11-01 Thread Gilles Filippini
Gilles Filippini a écrit le 31/10/2020 à 15:11 : > Hi Josh, > > Johannes 'josch' Schauer a écrit le 27/10/2020 à 18:45 : >> Package: libhdf5-openmpi-dev >> Version: 1.10.6+repack-2 >> Severity: wishlist >> >> Hi, >> >> when insta

Bug#973261: libhdf5-openmpi-dev: installing requires /proc being mounted

2020-10-31 Thread Gilles Filippini
Hi Josh, Johannes 'josch' Schauer a écrit le 27/10/2020 à 18:45 : > Package: libhdf5-openmpi-dev > Version: 1.10.6+repack-2 > Severity: wishlist > > Hi, > > when installing libhdf5-openmpi-dev in a chroot that doesn't have /proc > mounted, one will get the following error: > > Setting up libhdf

Bug#969633: transition: json-simple

2020-09-20 Thread Gilles Filippini
Hi Emilio, Emilio Pozuelo Monfort a écrit le 20/09/2020 à 18:50 : > On 06/09/2020 13:38, Gilles Filippini wrote: >> Emilio Pozuelo Monfort a écrit le 06/09/2020 à 12:19 : >>> On 06/09/2020 11:53, Gilles Filippini wrote: >>>> Package: release.debian.org &

Bug#969633: transition: json-simple

2020-09-06 Thread Gilles Filippini
Emilio Pozuelo Monfort a écrit le 06/09/2020 à 12:19 : > On 06/09/2020 11:53, Gilles Filippini wrote: >> Package: release.debian.org >> Severity: normal >> User: release.debian@packages.debian.org >> Usertags: transition >> >> Hi, >> >>

Bug#969633: transition: json-simple

2020-09-06 Thread Gilles Filippini
Package: release.debian.org Severity: normal User: release.debian@packages.debian.org Usertags: transition -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, I'd like to transition json-simple 3.1.1 surrently sitting into experimental. The name of the library doens't change, but reverse dep

Bug#968937: src:derby: Please add support to build against libjson-simple-java >= 3

2020-09-05 Thread Gilles Filippini
tony mancill a écrit le 05/09/2020 à 22:29 : > One more comment on the patch for this bug... > > It's a little odd that we're patching the build system for a specific > version of json-simple *at build time* when none of the binary packages > declares a dependency on this. > > For a short period

Bug#968937: src:derby: Please add support to build against libjson-simple-java >= 3

2020-09-05 Thread Gilles Filippini
Hi Emmanuel, Could you please review / apply this patch? Derby is the last blocker for this json-simple transition. Thanks in advance. _g. On Mon, 24 Aug 2020 10:37:35 +0200 Gilles Filippini wrote: > Package: src:derby > Version: 10.14.2.0-1 > Severity: normal > Tags: patch >

Bug#968937: src:derby: Please add support to build against libjson-simple-java >= 3

2020-08-24 Thread Gilles Filippini
g --- derby-10.14.2.0/debian/changelog2018-05-16 18:01:03.0 +0200 +++ derby-10.14.2.0/debian/changelog2020-08-24 09:49:39.0 +0200 @@ -1,3 +1,10 @@ +derby (10.14.2.0-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Tentative support for json-simple >= 3 + + -

Bug#962560: code-saturne built-in file editor fails

2020-06-16 Thread Gilles Filippini
Hi Clinton, On Tue, 9 Jun 2020 14:08:12 -0700 Clinton Winant wrote: > Package: code-saturne > Version: 6.0 > > Severity: grave - makes the package unusable or mostly so: output in > built-in editor causes SaturneGUI to crash > > When I try to examine output files with the code-saturne bu

Bug#960589: src:i2p: Please add support to build against libjson-simple-java >= 3

2020-05-30 Thread Gilles Filippini
Hi, On Thu, 14 May 2020 19:42:37 +0200 Gilles Filippini wrote: > On Thu, 14 May 2020 12:38:36 +0200 Gilles Filippini wrote: > > Package: src:i2p > > Version: 0.9.45-1 > > Severity: normal > > Tags: patch > > > > Hi, > > > > I'd like t

Bug#960639: Bug#960639: src:orthanc-imagej: Please add support to build against libjson-simple-java >= 3

2020-05-28 Thread Gilles Filippini
Sébastien Jodogne a écrit le 28/05/2020 à 11:28 : > Dear Gilles, > > I finally managed to find a few hours to finalize your patch. I had to > extend it a bit so for it to work correctly [1]. > > Version "1.2+dfsg-2" of the package has just been uploaded accordingly. Thanks!! Best, _ni.

Bug#960632: src:plm: Please add support to build against libjson-simple-java >= 3

2020-05-17 Thread Gilles Filippini
Gilles Filippini a écrit le 17/05/2020 à 23:29 : > Gilles Filippini a écrit le 17/05/2020 à 22:51 : >> Hi Martin, >> >> Martin Quinson a écrit le 17/05/2020 à 22:31 : >>> Hello again, >>> >>> when I try to launch the program with your

Bug#960632: src:plm: Please add support to build against libjson-simple-java >= 3

2020-05-17 Thread Gilles Filippini
Gilles Filippini a écrit le 17/05/2020 à 22:51 : > Hi Martin, > > Martin Quinson a écrit le 17/05/2020 à 22:31 : >> Hello again, >> >> when I try to launch the program with your patch applied, I get the >> following backtrace: >> >> Exception in thre

Bug#960632: src:plm: Please add support to build against libjson-simple-java >= 3

2020-05-17 Thread Gilles Filippini
Hi Martin, Martin Quinson a écrit le 17/05/2020 à 22:31 : > Hello again, > > when I try to launch the program with your patch applied, I get the > following backtrace: > > Exception in thread "main" java.lang.ClassCastException: class > org.json.simple.JsonArray cannot be cast to class > org.jso

Bug#960639: Bug#960639: src:orthanc-imagej: Please add support to build against libjson-simple-java >= 3

2020-05-15 Thread Gilles Filippini
Andreas Tille a écrit le 15/05/2020 à 12:49 : > Hi Sébastien, > > On Fri, May 15, 2020 at 07:50:01AM +0200, Sébastien Jodogne wrote: >> As far as I'm concerned, I don't have time to have a look at this >> problem in the upstream project before several months. The Orthanc >> project is indeed under

Bug#960692: src:netbeans: Please add support to build against libjson-simple-java >= 3

2020-05-15 Thread Gilles Filippini
Package: src:netbeans Version: 10.0-3 Severity: normal Tags: patch -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, I'd like to transition json-simple 3.1.1 to unstable, but netbeans is a blocker since it builds against libjson-simple-java << 3 only. The json-simple classes used by netbeans

Bug#960654: [Debian-med-packaging] Bug#960654: src:biojava4-live: Please add support to build against libjson-simple-java >= 3

2020-05-15 Thread Gilles Filippini
Hi Olivier, olivier sallou a écrit le 15/05/2020 à 10:59 : > Hi, > thanks for the patch. > However, if json-simple API/ABI is broken, I think that package should > be kinda libjson-simple3-java to keep compatibility with existing > packages using old versions and allow transition of packages to ne

Bug#960654: src:biojava4-live: Please add support to build against libjson-simple-java >= 3

2020-05-15 Thread Gilles Filippini
edium + + * Non-maintainer upload. + * Tentative fix to build against json-simple 3 + + -- Gilles Filippini Fri, 15 May 2020 08:50:46 +0200 + biojava4-live (4.2.12+dfsg-2) unstable; urgency=medium * Team upload. diff -Nru biojava4-live-4.2.12+dfsg/debian/patches/use_simple_json biojava4-live-4.

Bug#960652: src:jts: Please add support to build against libjson-simple-java >= 3

2020-05-14 Thread Gilles Filippini
substituted at build time by debian/rules. + . + With these tricks the package is compatible with json-simple 2.x and 3.x. +Author: Gilles Filippini +Index: jts-1.16.1+ds/modules/io/common/src/main/java/org/locationtech/jts/i

Bug#960639: src:orthanc-imagej: Please add support to build against libjson-simple-java >= 3

2020-05-14 Thread Gilles Filippini
ncy=medium + + * Non-maintainer upload. + * tentative patch to build against json-simple 3 + + -- Gilles Filippini Thu, 14 May 2020 23:29:49 +0200 + orthanc-imagej (1.2+dfsg-1) unstable; urgency=medium * New upstream version. (Closes: #912363) diff -Nru orthanc-imagej-1.2+dfsg/debian/patche

Bug#960632: src:plm: Please add support to build against libjson-simple-java >= 3

2020-05-14 Thread Gilles Filippini
against json-simple 3 + + -- Gilles Filippini Thu, 14 May 2020 18:05:12 +0200 + plm (2.6+repack-3) unstable; urgency=medium * Add run-time dependencies on default-jdk, jython and jruby. diff -Nru plm-2.6+repack/debian/patches/json-simple-3.patch plm-2.6+repack/debian/patches/json-simple-3.patch ---

Bug#960589: src:i2p: Please add support to build against libjson-simple-java >= 3

2020-05-14 Thread Gilles Filippini
On Thu, 14 May 2020 12:38:36 +0200 Gilles Filippini wrote: > Package: src:i2p > Version: 0.9.45-1 > Severity: normal > Tags: patch > > Hi, > > I'd like to transition json-simple 3.1.1 to unstable, but i2p is a blocker > since it builds against libjson-simple-java

Bug#960612: src:tika: Please add support to build against libjson-simple-java >= 3

2020-05-14 Thread Gilles Filippini
--- tika-1.22/debian/changelog 2019-08-05 11:41:25.0 +0200 +++ tika-1.22/debian/changelog 2020-05-14 15:14:44.0 +0200 @@ -1,3 +1,10 @@ +tika (1.22-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Tentative patch to build against json-simple >= 3 + + -- Gilles Fili

Bug#960589: src:i2p: Please add support to build against libjson-simple-java >= 3

2020-05-14 Thread Gilles Filippini
--- i2p-0.9.45/debian/changelog 2020-04-12 16:50:00.0 +0200 +++ i2p-0.9.45/debian/changelog 2020-05-13 11:12:38.0 +0200 @@ -1,3 +1,10 @@ +i2p (0.9.45-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Tentative support for json-simple >= 3 + + -- Gilles Filippini W

Bug#955694: scilab: FTBFS: Scilab cannot create Scilab Java Main-Class (we have not been able to find the main Scilab class. Check if the Scilab and thirdparty packages are available).

2020-04-30 Thread Gilles Filippini
Control: found -1 5.5.2-4 Control: found -1 6.0.1-10 Julien Puydt a écrit le 23/04/2020 à 09:37 : > Hi, > > Le jeudi 23 avril 2020 à 00:20 +0200, Gilles Filippini a écrit : >> Gilles Filippini a écrit le 22/04/2020 à 09:59 : >>> I think I've eventually found

Bug#949780: maptool: Maptool segfaults

2020-04-24 Thread Gilles Filippini
Gilles Filippini a écrit le 24/04/2020 à 15:08 : > On Sun, 26 Jan 2020 12:39:01 + ael wrote: >> On Sat, Jan 25, 2020 at 06:26:35PM -0800, Joseph Herlant wrote: >>> Hi, >>> >>> >>> You mention in the bug there that you were able to run your pbf by

Bug#949780: maptool: Maptool segfaults

2020-04-24 Thread Gilles Filippini
On Sun, 26 Jan 2020 12:39:01 + ael wrote: > On Sat, Jan 25, 2020 at 06:26:35PM -0800, Joseph Herlant wrote: > > Hi, > > > > > > You mention in the bug there that you were able to run your pbf by > > compiling maptool from the git repo. What compilation flags did you > > use? > > I just real

Bug#958174: hdf5: please add the hdf5plugins

2020-04-24 Thread Gilles Filippini
picca a écrit le 22/04/2020 à 16:07 : > Gilles Filippini writes: > >> Aren't most of these filters available in the pytables and bitshuffle >> packages? > > It seems to me that these filters are provided but not installed system > wide under the hdf5 plugin

Bug#958530: sqlite3: Please configure a default search path to load extensions from

2020-04-23 Thread Gilles Filippini
Package: sqlite3 Version: 3.31.1-4 Severity: wishlist -BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Hi, The load_extension feature of sqlite3 searchs for the specified extensions into the system's default path for shared libraries. But these extensions shouldn't be installed into these paths b

Bug#955694: scilab: FTBFS: Scilab cannot create Scilab Java Main-Class (we have not been able to find the main Scilab class. Check if the Scilab and thirdparty packages are available).

2020-04-22 Thread Gilles Filippini
Control: tag -1 + patch Gilles Filippini a écrit le 22/04/2020 à 19:35 : > Gilles Filippini a écrit le 22/04/2020 à 09:59 : >> Hi, >> >> Matthias Klose a écrit le 20/04/2020 à 12:49 : >>> On 4/20/20 11:52 AM, Gilles Filippini wrote: >>>> I'd like to

Bug#955694: scilab: FTBFS: Scilab cannot create Scilab Java Main-Class (we have not been able to find the main Scilab class. Check if the Scilab and thirdparty packages are available).

2020-04-22 Thread Gilles Filippini
Gilles Filippini a écrit le 22/04/2020 à 09:59 : > Hi, > > Matthias Klose a écrit le 20/04/2020 à 12:49 : >> On 4/20/20 11:52 AM, Gilles Filippini wrote: >>> I'd like to do a bisect between openjdk-11 11.0.6+10-2 and 11.0.7+9-1 to >>> better under

Bug#958174: hdf5: please add the hdf5plugins

2020-04-22 Thread Gilles Filippini
Hi Frédéric, Picca Frédéric-Emmanuel a écrit le 19/04/2020 à 12:41 : > > Source: hdf5 > Severity: normal > > Dear Maintainer, > > I saw on the hdf5 group website that they provide also hdf5plugin > > https://www.hdfgroup.org/downloads/hdf5/ > > Is it possible to add these plugins in the hdf5

Bug#955694: scilab: FTBFS: Scilab cannot create Scilab Java Main-Class (we have not been able to find the main Scilab class. Check if the Scilab and thirdparty packages are available).

2020-04-22 Thread Gilles Filippini
Hi, Matthias Klose a écrit le 20/04/2020 à 12:49 : > On 4/20/20 11:52 AM, Gilles Filippini wrote: >> I'd like to do a bisect between openjdk-11 11.0.6+10-2 and 11.0.7+9-1 to >> better understand the problem but I can't find the corresponding branch >> on the op

Bug#955694: scilab: FTBFS: Scilab cannot create Scilab Java Main-Class (we have not been able to find the main Scilab class. Check if the Scilab and thirdparty packages are available).

2020-04-20 Thread Gilles Filippini
Control: tags -1 + help Lucas Nussbaum a écrit le 03/04/2020 à 21:55 : > Source: scilab > Version: 6.1.0+dfsg1-1 > Severity: serious > Justification: FTBFS on amd64 > Tags: bullseye sid ftbfs > Usertags: ftbfs-20200402 ftbfs-bullseye > > Hi, > > During a rebuild of all packages in sid, your pack

Bug#955456: bitshuffle: diff for NMU version 0.3.5-3.1

2020-04-07 Thread Gilles Filippini
gelog --- bitshuffle-0.3.5/debian/changelog 2019-12-01 19:03:38.0 +0100 +++ bitshuffle-0.3.5/debian/changelog 2020-04-07 20:50:47.0 +0200 @@ -1,3 +1,21 @@ +bitshuffle (0.3.5-3.1) unstable; urgency=medium + + * Non-maintainer upload. + + [ Drew Parsons , Gilles Filippini ] + * C

Bug#955456: FTBFS: test file tmp_test_filters.h5 does not exist

2020-04-06 Thread Gilles Filippini
Control: tags -1 + patch Gilles Filippini a écrit le 06/04/2020 à 14:23 : > Drew Parsons a écrit le 06/04/2020 à 05:08 : >> On 2020-04-06 09:56, Drew Parsons wrote: >>> On 2020-04-06 01:48, Gilles Filippini wrote: >>>> Drew Parsons a écrit le 05/04/2020 à 18:57 : &g

Bug#955456: FTBFS: test file tmp_test_filters.h5 does not exist

2020-04-06 Thread Gilles Filippini
Drew Parsons a écrit le 06/04/2020 à 05:08 : > On 2020-04-06 09:56, Drew Parsons wrote: >> On 2020-04-06 01:48, Gilles Filippini wrote: >>> Drew Parsons a écrit le 05/04/2020 à 18:57 : >>>> >>>> Another option is to create an environment variable to fo

Bug#955456: FTBFS: test file tmp_test_filters.h5 does not exist

2020-04-05 Thread Gilles Filippini
Drew Parsons a écrit le 05/04/2020 à 18:57 : > On 2020-04-05 22:34, Gilles Filippini wrote: >> I suspect a mismatch between mpi and serial build-depdencies: >> >> python3-h5py-serial + libhdf5-dev    => OK >> python3-h5py-serial + libhdf5-openmpi-dev    => KO

Bug#955456: FTBFS: test file tmp_test_filters.h5 does not exist

2020-04-05 Thread Gilles Filippini
Drew Parsons a écrit le 05/04/2020 à 15:28 : > On 2020-04-05 20:38, Gilles Filippini wrote: >>> >>> But it must be something else from these new h5py upstream patches >>> that's leading to any other bitshuffle errors (the ones apart from the >>> file-no

Bug#955456: FTBFS: test file tmp_test_filters.h5 does not exist

2020-04-05 Thread Gilles Filippini
Drew Parsons a écrit le 03/04/2020 à 15:08 : > On 2020-04-03 20:13, Gilles Filippini wrote: >> >> This is not related to the ongoing hdf5 transition, but to the recent >> uploads of h5py >= 2.10.0-3. Before triggering the hdf5 transition I've >> checked that bit

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