Source: libpdl-io-hdf5-perl Version: 1:0.73-4 Severity: important Tags: patch
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Hi, libpdl-io-hdf5-perl FTBFS against HDF5 1.10.3 currently in experimental: make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_test -O--parallel make -j5 test TEST_VERBOSE=1 make[1]: Entering directory '/<<PKGBUILDDIR>>' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HDF5.bs blib/arch/auto/PDL/IO/HDF5/HDF5.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t HDF5-DIAG: Error detected in HDF5 (1.10.3) thread 140450522435520: #000: ../../../src/H5Ddeprec.c line 257 in H5Dextend(): unable to extend dataset major: Dataset minor: Unable to initialize object #001: ../../../src/H5Dint.c line 2603 in H5D__set_extent(): dataset has contiguous storage major: Invalid arguments to routine minor: Out of range Error extending dataset in PDL::IO::HDF5::Dataset:set at t/attribPDL.t line 33. # Failed test at t/attribPDL.t line 67. # Looks like you failed 1 test of 13. t/attribPDL.t ..... ... All failures are related to the error above, occuring during dataset creation. As I undertand it, in dataset->set(), the dataset is first created, then extended to store the data. In HDF5 1.10.3, dataset extension now relies on H5D__set_extent() where we have: /* Check if we are allowed to modify the space; only datasets with chunked and external storage are allowed to be modified */ if(H5D_COMPACT == dset->shared->layout.type) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "dataset has compact storage") if(H5D_CONTIGUOUS == dset->shared->layout.type && 0 == dset->shared->dcpl_cache.efl.nused) HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "dataset has contiguous storage") The attached patch fixes the failing tests by creating the datasets with the option 'unlimited' to workaround the problem. Thanks, _g. - -- System Information: Distributor ID: PureOS Description: PureOS GNU/Linux 8 Release: 8 Codename: green Architecture: x86_64 Kernel: Linux 4.14.0-3-amd64 (SMP w/4 CPU cores) Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAlvN1GQACgkQ7+hsbH/+ z4OGVQf8CMu/FyaZn35Z63qmZ6fKGS+ba24kifwHexnAnbDCtU16V8wO/oykgJH0 qbdztqGexfRK6rrYcdb1tC2/P790CrPaTREUwMWqyYudOQpA24uX6SqaH4W2MbYX KYe1YBG5KfaN5m7tUiAoMc5DtZOreo5jk/++77g9Ygx9BMm8LxjN9pVab41GD3VW 4ACyJFLt9Q6Iv2SC0jq91Ssb1+N3kbDT8Pm8ty645sMgoJhWxDV0wWroZe0cPAx8 ZbgXZ2vYf7k2TH5uLbblqvwgsngMB/uE+nwxvFqWXeR3wOqiJqSjXCdmeughqXZn 9XngiQEzBC+ihYL4LTnYkJStBarW6g== =bbcn -----END PGP SIGNATURE-----
diff -Nru libpdl-io-hdf5-perl-0.73/debian/changelog libpdl-io-hdf5-perl-0.73/debian/changelog --- libpdl-io-hdf5-perl-0.73/debian/changelog 2018-07-22 19:38:40.000000000 +0200 +++ libpdl-io-hdf5-perl-0.73/debian/changelog 2018-10-22 15:30:22.000000000 +0200 @@ -1,3 +1,10 @@ +libpdl-io-hdf5-perl (1:0.73-4.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * New patch to support HDF5-1.10.3 + + -- Gilles Filippini <p...@debian.org> Mon, 22 Oct 2018 15:30:22 +0200 + libpdl-io-hdf5-perl (1:0.73-4) unstable; urgency=medium * Team upload. diff -Nru libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch --- libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch 1970-01-01 01:00:00.000000000 +0100 +++ libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch 2018-10-22 15:02:03.000000000 +0200 @@ -0,0 +1,79 @@ +Index: libpdl-io-hdf5-perl-0.73/t/attribPDL.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/attribPDL.t ++++ libpdl-io-hdf5-perl-0.73/t/attribPDL.t +@@ -30,7 +30,7 @@ my $group=$hdf5->group('Radiometric info + + # Store a dataset + my $dataset=$group->dataset('SP_BT'); +-$dataset->set($bt); ++$dataset->set($bt, unlimited => 1); + + # Store a scalar and pdl attribute + $dataset->attrSet('UNITS'=>'K'); +Index: libpdl-io-hdf5-perl-0.73/t/group.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/group.t ++++ libpdl-io-hdf5-perl-0.73/t/group.t +@@ -78,7 +78,7 @@ my $dataset = new PDL::IO::HDF5::Dataset + my $pdl = sequence(5,4); + + +-ok( $dataset->set($pdl) ); ++ok( $dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + +Index: libpdl-io-hdf5-perl-0.73/t/reference.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/reference.t ++++ libpdl-io-hdf5-perl-0.73/t/reference.t +@@ -18,7 +18,7 @@ my $group=$hdf5->group('group1'); + # Store a dataset + my $dataset=$hdf5->dataset('data1'); + my $data = pdl [ 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0 ]; +-$dataset->set($data); ++$dataset->set($data, unlimited => 1); + + # create the reference + my @regionStart = ( 3 ); +Index: libpdl-io-hdf5-perl-0.73/t/total.t +=================================================================== +--- libpdl-io-hdf5-perl-0.73.orig/t/total.t ++++ libpdl-io-hdf5-perl-0.73/t/total.t +@@ -52,7 +52,7 @@ my $dataset = $hdfobj->dataset('rootdata + my $pdl = sequence(5,4); + + +-ok($dataset->set($pdl) ); ++ok($dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + # Create String dataset using PDL::Char +@@ -60,7 +60,7 @@ my $dataset2 = $hdfobj->dataset('charDat + + my $pdlChar = new PDL::Char( [ ["abccc", "def", "ghi"],["jkl", "mno", 'pqr'] ] ); + +-ok($dataset2->set($pdlChar)); ++ok($dataset2->set($pdlChar, unlimited => 1)); + + + my $pdl2 = $dataset->get; +@@ -92,7 +92,7 @@ $dataset = $subgroup->dataset('my datase + $pdl = sequence(5,4)->float; # Try a non-default data type + + +-ok( $dataset->set($pdl) ); ++ok( $dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + +@@ -119,7 +119,7 @@ $dataset = $subgroup->dataset('my datase + $pdl = sequence(5,4)->long; # Try a non-default data type + + +-ok( $dataset->set($pdl) ); ++ok( $dataset->set($pdl, unlimited => 1) ); + # print "pdl written = \n".$pdl."\n"; + + diff -Nru libpdl-io-hdf5-perl-0.73/debian/patches/series libpdl-io-hdf5-perl-0.73/debian/patches/series --- libpdl-io-hdf5-perl-0.73/debian/patches/series 2016-10-24 22:41:04.000000000 +0200 +++ libpdl-io-hdf5-perl-0.73/debian/patches/series 2018-10-22 14:58:43.000000000 +0200 @@ -4,3 +4,4 @@ reproducible_build.patch spelling-errors.patch hdf5-1.10.patch +hdf5-1.10.3.patch