Source: libpdl-io-hdf5-perl
Version: 1:0.73-4
Severity: important
Tags: patch
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Hash: SHA512
Hi,
libpdl-io-hdf5-perl FTBFS against HDF5 1.10.3 currently in experimental:
make[1]: Leaving directory '/<>'
dh_auto_test -O--parallel
make -j5 test TEST_VERBOSE=1
make[1]: Entering directory '/<>'
"/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
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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 19:38:40.0
+0200
+++ libpdl-io-hdf5-perl-0.73/debian/changelog 2018-10-22 15:30:22.0
+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 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
01:00:00.0 +0100
+++ libpdl-io-hdf5-perl-0.73/debian/patches/hdf5-1.10.3.patch 2018-10-22
15:02:03.0 +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
