Bug#911609: libpdl-io-hdf5-perl: FTBFS with HDF5 1.10.3

Gilles Filippini pini at debian.org
Mon Oct 22 14:45:17 BST 2018 

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-----
-------------- next part --------------
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 <pini at 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

More information about the pkg-perl-maintainers mailing list