Bug#861736: closed by Andreas Tille <tille at debian.org> (Bug#861736: fixed in nexus 4.3.2-svn1921-5)

[Gilles Filippini]

Control: tags -1 + patch

Hi,

On Fri, 12 May 2017 08:32:28 +0200 Marc Rosanes <mrosanes at cells.es> wrote:
> Hi,
> 
> We have found that python-nxs is still affected by problems:
> 
> The following piece of code fails on stretch + the lastest nexus from 
> unstable:
> 
> ```
> import nxs
> f = nxs.open("/tmp/foo.h5", "w5")
> f.makegroup('entry', 'NXentry')
> f.opengroup('entry')
> f.makegroup('g', 'NXcollection')
> f.opengroup('g', 'NXcollection')
> f.makedata('d', 'float64', shape=(1,))
> f.opendata('d')
> f.putdata(1.23)
> f.closedata()
> f.closegroup()
> f.flush()
> f.close()
> ```
> 
> 
> It fails with the exception:
> 
> ```
> Traceback (most recent call last):
>    File "nxs_flush_bug.py", line 12, in <module>
>      f.flush()
>    File "/usr/lib/python2.7/dist-packages/nxs/napi.py", line 397, in flush
>      raise NeXusError, "Could not flush NeXus file %s"%(self.filename)
> nxs.napi.NeXusError: Could not flush NeXus file /tmp/foo.h5
> ```
> 
> 
> The same code works correctly on a clean jessie docker.
> 
> This ticket should be reopened, till this issue is solved.
> 
> 
> 
> 
> On 05/11/2017 11:12 AM, Debian Bug Tracking System wrote:
> > This is an automatic notification regarding your Bug report
> > which was filed against the python-nxs package:
> >
> > #861736: python-nxs: Cannot save files with nxs python module
> >
> > It has been closed by Andreas Tille <tille at debian.org>.
> >
> > Their explanation is attached below along with your original report.
> > If this explanation is unsatisfactory and you have not received a
> > better one in a separate message then please contact Andreas Tille <tille at debian.org> by
> > replying to this email.

New patch proposal attached. It fixes #866925 as well.

Thanks,

_g.
-------------- next part --------------
diff -Nru nexus-4.3.2-svn1921/debian/changelog nexus-4.3.2-svn1921/debian/changelog
--- nexus-4.3.2-svn1921/debian/changelog	2017-05-11 09:23:17.000000000 +0200
+++ nexus-4.3.2-svn1921/debian/changelog	2017-10-11 19:15:12.000000000 +0200
@@ -1,3 +1,12 @@
+nexus (4.3.2-svn1921-5.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * debian/control: switch B-D from libhdf4g-dev to libhdf4-dev (closes:
+    #866925)
+  * Fix patch hdf5-1.10-support.patch (closes: #861736)
+
+ -- Gilles Filippini <pini at debian.org>  Wed, 11 Oct 2017 19:15:12 +0200
+
 nexus (4.3.2-svn1921-5) unstable; urgency=medium
 
   * Team upload.
diff -Nru nexus-4.3.2-svn1921/debian/control nexus-4.3.2-svn1921/debian/control
--- nexus-4.3.2-svn1921/debian/control	2017-05-11 09:23:17.000000000 +0200
+++ nexus-4.3.2-svn1921/debian/control	2017-10-11 19:15:10.000000000 +0200
@@ -8,7 +8,7 @@
                debhelper (>= 7),
                default-jdk | java2-sdk,
                dh-python,
-               libhdf4g-dev,
+               libhdf4-dev,
                libhdf5-dev,
                libmxml-dev,
                libtool,
diff -Nru nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch
--- nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch	2017-05-11 09:23:17.000000000 +0200
+++ nexus-4.3.2-svn1921/debian/patches/hdf5-1.10-support.patch	2017-10-11 19:15:12.000000000 +0200
@@ -1,11 +1,16 @@
 Description: HDF5 1.10.x uses 64 bit handles. They're not int anymore.
 Author: Gilles Filippini <pini at debian.org>
 Bug-Debian: https://bugs.debian.org/861736
-Index: nexus-4.3.2-svn1921/src/napi5.c
+Index: nexus/src/napi5.c
 ===================================================================
---- nexus-4.3.2-svn1921.orig/src/napi5.c
-+++ nexus-4.3.2-svn1921/src/napi5.c
-@@ -54,12 +54,12 @@ extern  void *NXpData;
+--- nexus.orig/src/napi5.c
++++ nexus/src/napi5.c
+@@ -50,16 +50,16 @@ extern  void *NXpData;
+   typedef struct __NexusFile5 {
+         struct iStack5 {
+           char irefn[1024];
+-          int iVref;
++          hid_t iVref;
            hsize_t iCurrentIDX;
          } iStack5[NXMAXSTACK];
          struct iStack5 iAtt5;
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 508 bytes
Desc: OpenPGP digital signature
URL: <http://lists.alioth.debian.org/pipermail/debian-science-maintainers/attachments/20171016/11d12dd2/attachment.sig>