Bug#802321: gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal

[Sebastiaan Couwenberg]

Control: tags -1 unreproducible
Control: severity -1 important

Hi Otakar,

Thanks for the nc file, can you also send the files used by gmt?

With JEJK_topoC9k_ZABA10mHbpv.nc I can now confirm that the issue is not
present in gdal (1.11.2+dfsg-3+b2) on unstable:

$ ncdump -h JEJK_topoC9k_ZABA10mHbpv.nc
netcdf JEJK_topoC9k_ZABA10mHbpv {
dimensions:
x = 501 ;
y = 601 ;
variables:
double x(x) ;
x:long_name = "x" ;
x:actual_range = -546000., -541000. ;
double y(y) ;
y:long_name = "y" ;
y:actual_range = -1073000., -1067000. ;
float z(y, x) ;
z:long_name = "z" ;
z:_FillValue = NaNf ;
z:actual_range = 2.38614749908447, 11.5756139755249 ;

// global attributes:
:Conventions = "COARDS, CF-1.5" ;
:title = "Produced by grdreformat" ;
:history = "grdreformat CRJK_topoC9c_ZABAGED10m.grd
Jesenik_topoC9_ZABAGED10mBpv.nc -R-546000/-541000/-1073000/-1067000" ;
:GMT_version = "5.1.2 (r14256) [64-bit]" ;
}

$ ncdump -k JEJK_topoC9k_ZABA10mHbpv.nc
netCDF-4

$ h5dump -n JEJK_topoC9k_ZABA10mHbpv.nc
HDF5 "JEJK_topoC9k_ZABA10mHbpv.nc" {
FILE_CONTENTS {
 group  /
 dataset/x
 dataset/y
 dataset/z
 }
}

$ gdalinfo JEJK_topoC9k_ZABA10mHbpv.nc
Driver: netCDF/Network Common Data Format
Files: JEJK_topoC9k_ZABA10mHbpv.nc
Size is 501, 601
Coordinate System is `'
Origin = (-546005.000,-1066995.000)
Pixel Size = (10.000,-10.000)
Metadata:
  NC_GLOBAL#Conventions=COARDS, CF-1.5
  NC_GLOBAL#GMT_version=5.1.2 (r14256) [64-bit]
  NC_GLOBAL#history=grdreformat CRJK_topoC9c_ZABAGED10m.grd
Jesenik_topoC9_ZABAGED10mBpv.nc -R-546000/-541000/-1073000/-1067000
  NC_GLOBAL#title=Produced by grdreformat
  x#actual_range={-546000,-541000}
  x#long_name=x
  y#actual_range={-1073000,-1067000}
  y#long_name=y
  z#_FillValue=nan
  z#actual_range={2.386147499084473,11.5756139755249}
  z#long_name=z
Corner Coordinates:
Upper Left  ( -546005.000,-1066995.000)
Lower Left  ( -546005.000,-1073005.000)
Upper Right ( -540995.000,-1066995.000)
Lower Right ( -540995.000,-1073005.000)
Center  ( -543500.000,-107.000)
Band 1 Block=167x151 Type=Float32, ColorInterp=Undefined
  NoData Value=nan
  Metadata:
_FillValue=nan
actual_range={2.386147499084473,11.5756139755249}
long_name=z
NETCDF_VARNAME=z

$ gmt grdreformat JEJK_topoC9k_ZABA10mHbpv.grd
JEJK_topoC9k_ZABA10mHbpv.xnc=nf
grdreformat: Error for input file: No such file
(JEJK_topoC9k_ZABA10mHbpv.grd)
grdreformat: Syntax error: Specify only one input and one output file

$ gmt grdinfo JEJK_topoC9k_ZABA10mHbpv.nc
JEJK_topoC9k_ZABA10mHbpv.nc: Title: Produced by grdreformat
JEJK_topoC9k_ZABA10mHbpv.nc: Command: grdreformat
CRJK_topoC9c_ZABAGED10m.grd Jesenik_topoC9_ZABAGED10mBpv.nc
-R-546000/-541000/-1073000/-1067000
JEJK_topoC9k_ZABA10mHbpv.nc: Remark:
JEJK_topoC9k_ZABA10mHbpv.nc: Gridline node registration used [Cartesian
grid]
JEJK_topoC9k_ZABA10mHbpv.nc: Grid file format: nf = GMT netCDF format
(32-bit float), COARDS, CF-1.5
JEJK_topoC9k_ZABA10mHbpv.nc: x_min: -546000 x_max: -541000 x_inc: 10
name: x nx: 501
JEJK_topoC9k_ZABA10mHbpv.nc: y_min: -1073000 y_max: -1067000 y_inc: 10
name: y ny: 601
JEJK_topoC9k_ZABA10mHbpv.nc: z_min: 2.38614749908 z_max: 11.5756139755
name: z
JEJK_topoC9k_ZABA10mHbpv.nc: scale_factor: 1 add_offset: 0
JEJK_topoC9k_ZABA10mHbpv.nc: format: netCDF-4 chunk_size: 167,151
shuffle: on deflation_level: 3

$ gmt grdinfo JEJK_topoC9k_ZABA10mHbpv.nc=gd
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 0, Y offset 0
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 1, Y offset 0
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 2, Y offset 0
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 0, Y offset 1
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 1, Y offset 1
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 2, Y offset 1
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 0, Y offset 2
ERROR 1: nBlockYSize = 151, only 1 supported when reading bottom-up dataset
ERROR 1: JEJK_topoC9k_ZABA10mHbpv.nc, band 1: IReadBlock failed at X
offset 1, Y offset 2
ERROR 1: nBlockYSize = 151, only 1 supported 

Bug#802321: gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal

[otas]

Hi Bas,

On Mon, 19 Oct 2015 20:00:06 +0200, Sebastiaan Couwenberg wrote:
Do you have another testing machine perhaps that hasn't been updated 
yet?



Unfortunately not.

The issue is related to GMT 5.1.2 I'm using "in production" on my 
system (Debian Stretch). I have a MS Windows computer too with GMT 5.1, 
where the issue with NetCDF-4 format is not present.


Under wheezy, there is GMT 4.5.7 which is not so far dependent on gdal.
So I can issue under wheezy (on the same sample grid)

$ GMT grdinfo JEJK_topoC9k_ZABA10mHbpv.nc
JEJK_topoC9k_ZABA10mHbpv.nc: Title: Produced by grdreformat
JEJK_topoC9k_ZABA10mHbpv.nc: Command: grdreformat 
CRJK_topoC9c_ZABAGED10m.grd Jesenik_topoC9_ZABAGED10mBpv.nc 
-R-546000/-541000/-1073000/-1067000

JEJK_topoC9k_ZABA10mHbpv.nc: Remark:
JEJK_topoC9k_ZABA10mHbpv.nc: Gridline node registration used
JEJK_topoC9k_ZABA10mHbpv.nc: Grid file format: nf (# 18) GMT netCDF 
format (float)  (COARDS-compliant) [DEFAULT]
JEJK_topoC9k_ZABA10mHbpv.nc: x_min: -546000 x_max: -541000 x_inc: 10 
name: x nx: 501
JEJK_topoC9k_ZABA10mHbpv.nc: y_min: -1073000 y_max: -1067000 y_inc: 10 
name: y ny: 601
JEJK_topoC9k_ZABA10mHbpv.nc: z_min: 2.38614749908 z_max: 11.5756139755 
name: z

JEJK_topoC9k_ZABA10mHbpv.nc: scale_factor: 1 add_offset: 0

without any problem, because GMT4 applies directly own internal 
routines (or netcdf library functions) to recognize and import NetCDF-4 
raster data. However, the forced use of gdal input routines in GMT4 
brings a problem again (under wheezy):


$ GMT grdinfo JEJK_topoC9k_ZABA10mHbpv.nc=gd

terminates with SIGSEGV.

Take a closer look at gdal:

$ gdalinfo JEJK_topoC9k_ZABA10mHbpv.nc
HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
  #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
major: Dataset
minor: Object not found
  #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
object

major: Symbol table
minor: Object not found
  #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
path traversal failed

major: Symbol table
minor: Object not found
  #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): 
traversal operator failed

major: Symbol table
minor: Callback failed
  #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 
'xx' doesn't exist

major: Symbol table
minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
  #000: ../../../src/H5D.c line 391 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
  #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
major: Dataset
minor: Object not found
  #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
object

major: Symbol table
minor: Object not found
  #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
path traversal failed

major: Symbol table
minor: Object not found
  #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): 
traversal operator failed

major: Symbol table
minor: Callback failed
  #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 
'yy' doesn't exist

major: Symbol table
minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
  #000: ../../../src/H5D.c line 391 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
  #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
major: Dataset
minor: Object not found
  #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
object

major: Symbol table
minor: Object not found
  #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
path traversal failed

major: Symbol table
minor: Object not found
  #003: ../../../src/H5Gtraverse.c line 641 in H5G_traverse_real(): 
traversal operator failed

major: Symbol table
minor: Callback failed
  #004: ../../../src/H5Gloc.c line 385 in H5G_loc_find_cb(): object 
'zz' doesn't exist

major: Symbol table
minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
  #000: ../../../src/H5D.c line 391 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 140136550176640:
  #000: ../../../src/H5Ddeprec.c line 231 in H5Dopen1(): not found
major: Dataset
minor: Object not found
  #001: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find 
object

major: Symbol table
minor: Object not found
  #002: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal 
path traversal failed

major: Symbol table
minor: Object not found
  #003: ../../../src/H5Gtraverse.c 

Processed: Re: Bug#802462: libgdal1h: optional libpq5 dep

[Debian Bug Tracking System]

Processing control commands:

> tags -1 moreinfo
Bug #802462 [libgdal1h] libgdal1h: optional libpq5 dep
Added tag(s) moreinfo.

-- 
802462: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=802462
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

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Bug#802462: libgdal1h: optional libpq5 dep

[Bas Couwenberg]

Control: tags -1 moreinfo

Hi Julien,

Your bugreport lacks a body explaining the issue.

The subject "optional libpq5 dep" is not clear.

What is the actual issue you want to have addressed in the gdal package?

Kind Regards,

Bas

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Bug#802470: sumo: Fails to build with GDAL 2.0

[Bas Couwenberg]

Source: sumo
Version: 0.23.0+dfsg1-2
Severity: important
Tags: patch upstream
User: debian-...@lists.debian.org
Usertags: gdal-2.0

Dear Maintainer,

sumo (0.23.0+dfsg1-2) FTBFS due to missing compatibility with
GDAL/OGR 2.0:

 error: 'Open' is not a member of 'OGRSFDriverRegistrar'

This issue has been fixed upstream via #1868 with r18752:

 http://sumo.dlr.de/trac.wsgi/ticket/1868
 http://sumo.dlr.de/trac.wsgi/changeset/18752

The attached debdiff includes the changes from SVN r18752 in
50_gdal-2.0.patch, please consider including these changes in the next
sumo upload.

The severity of this issue will be increased to serious when the GDAL
2.0 transition starts.

There are no GDAL 2.0.1 packages available in experimental yet, because
the transition to GDAL 1.11.3 (#80) needs to start first. This issue
was triaged using locally built GDAL 2.0.1 packages from the
experimental-2.0 branch in git [1].

[0] https://lists.debian.org/debian-gis/2015/10/msg00022.html
[1]
http://anonscm.debian.org/cgit/pkg-grass/gdal.git/log/?h=experimental-2.0

Kind Regards,

Bas
diff -Nru sumo-0.23.0+dfsg1/debian/changelog sumo-0.23.0+dfsg1/debian/changelog
--- sumo-0.23.0+dfsg1/debian/changelog	2015-05-04 21:26:49.0 +0200
+++ sumo-0.23.0+dfsg1/debian/changelog	2015-10-20 12:53:22.0 +0200
@@ -1,3 +1,10 @@
+sumo (0.23.0+dfsg1-2.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Add patch for GDAL 2.0 support.
+
+ -- Bas Couwenberg   Tue, 20 Oct 2015 12:51:15 +0200
+
 sumo (0.23.0+dfsg1-2) unstable; urgency=medium
 
   * Move package from experimental to unstable
diff -Nru sumo-0.23.0+dfsg1/debian/patches/50_gdal-2.0.patch sumo-0.23.0+dfsg1/debian/patches/50_gdal-2.0.patch
--- sumo-0.23.0+dfsg1/debian/patches/50_gdal-2.0.patch	1970-01-01 01:00:00.0 +0100
+++ sumo-0.23.0+dfsg1/debian/patches/50_gdal-2.0.patch	2015-10-20 12:51:09.0 +0200
@@ -0,0 +1,65 @@
+Description: now supporting GDAL 2.0 (as well as 1.x).
+Author: Thomas Lockhart
+Bug: http://sumo.dlr.de/trac.wsgi/ticket/1868
+Origin: http://sumo.dlr.de/trac.wsgi/changeset/18752
+
+--- a/src/netbuild/NBHeightMapper.cpp
 b/src/netbuild/NBHeightMapper.cpp
+@@ -166,8 +166,13 @@ NBHeightMapper::loadIfSet(OptionsCont& o
+ int
+ NBHeightMapper::loadShapeFile(const std::string& file) {
+ #ifdef HAVE_GDAL
++#if GDAL_VERSION_MAJOR < 2
+ OGRRegisterAll();
+ OGRDataSource* ds = OGRSFDriverRegistrar::Open(file.c_str(), FALSE);
++#else
++GDALAllRegister();
++GDALDataset* ds = (GDALDataset*) GDALOpen(file.c_str(), GA_ReadOnly);
++#endif
+ if (ds == NULL) {
+ throw ProcessError("Could not open shape file '" + file + "'.");
+ }
+@@ -242,7 +247,11 @@ NBHeightMapper::loadShapeFile(const std:
+ */
+ OGRFeature::DestroyFeature(feature);
+ }
++#if GDAL_VERSION_MAJOR < 2
+ OGRDataSource::DestroyDataSource(ds);
++#else
++GDALClose(ds);
++#endif
+ OCTDestroyCoordinateTransformation(toWGS84);
+ OGRCleanupAll();
+ return numFeatures;
+--- a/src/netimport/NIImporter_ArcView.cpp
 b/src/netimport/NIImporter_ArcView.cpp
+@@ -125,8 +125,13 @@ void
+ NIImporter_ArcView::load() {
+ #ifdef HAVE_GDAL
+ PROGRESS_BEGIN_MESSAGE("Loading data from '" + mySHPName + "'");
++#if GDAL_VERSION_MAJOR < 2
+ OGRRegisterAll();
+ OGRDataSource* poDS = OGRSFDriverRegistrar::Open(mySHPName.c_str(), FALSE);
++#else
++GDALAllRegister();
++GDALDataset* poDS = (GDALDataset*) GDALOpen(mySHPName.c_str(), GA_ReadOnly);
++#endif
+ if (poDS == NULL) {
+ WRITE_ERROR("Could not open shape description '" + mySHPName + "'.");
+ return;
+--- a/src/polyconvert/PCLoaderArcView.cpp
 b/src/polyconvert/PCLoaderArcView.cpp
+@@ -84,8 +84,13 @@ PCLoaderArcView::load(const std::string&
+ bool useRunningID = oc.getBool("shapefile.use-running-id");
+ // start parsing
+ std::string shpName = file + ".shp";
++#if GDAL_VERSION_MAJOR < 2
+ OGRRegisterAll();
+ OGRDataSource* poDS = OGRSFDriverRegistrar::Open(shpName.c_str(), FALSE);
++#else
++GDALAllRegister();
++GDALDataset* poDS = (GDALDataset*) GDALOpen(shpName.c_str(), GA_ReadOnly);
++#endif
+ if (poDS == NULL) {
+ throw ProcessError("Could not open shape description '" + shpName + "'.");
+ }
diff -Nru sumo-0.23.0+dfsg1/debian/patches/series sumo-0.23.0+dfsg1/debian/patches/series
--- sumo-0.23.0+dfsg1/debian/patches/series	2015-05-04 21:24:34.0 +0200
+++ sumo-0.23.0+dfsg1/debian/patches/series	2015-10-20 12:53:14.0 +0200
@@ -2,3 +2,4 @@
 20_fix_scripts_headers.patch
 30_add_missing_link.patch
 40_drop_some_buildflags.patch
+50_gdal-2.0.patch
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Bug#802462: libgdal1h: optional libpq5 dep

[Julien Hebert]

Package: libgdal1h
Version: 1.10.1+dfsg-8+b3
Severity: normal

Dear Maintainer,

*** Reporter, please consider answering these questions, where appropriate ***

   * What led up to the situation?
   * What exactly did you do (or not do) that was effective (or
 ineffective)?
   * What was the outcome of this action?
   * What outcome did you expect instead?

*** End of the template - remove these template lines ***


-- System Information:
Debian Release: 8.2
  APT prefers stable
  APT policy: (990, 'stable'), (500, 'testing-proposed-updates'), (500, 
'proposed-updates'), (500, 'oldstable-updates'), (500, 
'oldstable-proposed-updates'), (500, 'oldstable'), (101, 'testing'), (100, 
'unstable'), (10, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/8 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages libgdal1h depends on:
ii  libarmadillo4 1:4.450.2+dfsg-1
ii  libc6 2.19-18+deb8u1
ii  libcurl3-gnutls   7.38.0-4+deb8u2
ii  libdap11  3.12.0-1
ii  libdapclient3 3.12.0-1
ii  libdapserver7 3.12.0-1
ii  libepsilon1   0.9.2-2
ii  libexpat1 2.1.0-6+deb8u1
ii  libfreexl11.0.0g-1+deb8u2
ii  libgcc1   1:4.9.2-10
ii  libgeos-c13.4.2-6
ii  libgif4   4.1.6-11
ii  libhdf4-0-alt 4.2.10-3
ii  libhdf5-8 1.8.13+docs-15
ii  libjasper11.900.1-debian1-2.4
ii  libjpeg62-turbo   1:1.3.1-12
ii  libkml0   1.3.0~r864+dfsg-1
ii  liblzma5  5.1.1alpha+20120614-2+b3
ii  libmysqlclient18  5.5.44-0+deb8u1
ii  libnetcdfc7   1:4.1.3-7.2
ii  libodbc1  2.3.1-3
ii  libogdi3.23.2.0~beta2-7.1
ii  libpng12-01.2.50-2+b2
ii  libpoppler46  0.26.5-2
ii  libpq59.4.4-0+deb8u1
ii  libproj0  4.8.0-5
ii  libspatialite54.1.1-10
ii  libstdc++64.9.2-10
ii  liburiparser1 0.8.0.1-2
ii  libwebp5  0.4.1-1.2+b2
ii  libxerces-c3.13.1.1-5.1
ii  libxml2   2.9.1+dfsg1-5
ii  odbcinst1debian2  2.3.1-3
ii  zlib1g1:1.2.8.dfsg-2+b1

Versions of packages libgdal1h recommends:
ii  proj-bin  4.8.0-5

libgdal1h suggests no packages.

-- no debconf information

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Bug#802321: gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal

[otas]

Hello Bas,

On Tue, 20 Oct 2015 09:06:02 +0200, Sebastiaan Couwenberg wrote:
With JEJK_topoC9k_ZABA10mHbpv.nc I can now confirm that the issue is 
not

present in gdal (1.11.2+dfsg-3+b2) on unstable:


thank you for the suggestion.
Since the full downgrade is difficult for me (due to dependencies of 
other software), I'd rather upgrade.


After short investigation I found the only related difference between 
unstable and testing in libnetcdf7.
And yes, it was there! When I upgraded just from libnetcdf7_4.4.0~rc2-1 
(testing) to libnetcdf7_4.4.0~rc2-1+b1 (unstable) it seems, all (in the 
chain) started to work correctly.


My current version of related packages shoud be the same as in 
unstable, i.e. gmt 5.1.2+dfsg1-2+b1, gdal and libgdal1i 
1.11.2+dfsg-3+b2, libhdf5-10 1.8.15-patch1+docs-4 and libnetcdf7 
1:4.4.0~rc2-1+b1.


Therefore, it seems to be just a temporary issue of testing, that 
should be solved with libnetcdf7_4.4.0~rc2-1+b1 migration.


So, one might consider to close the bug.
Meanwhile, just the dependence of libgdal1i could be restricted to an 
appropriate version of libnetcdf7, nevertheless, it is safe to ignore 
this issue completely, because just a 'temporary' libnetcdf7_4.4.0~rc2-1 
seems to be broken.


Best regards,

Otakar

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Processed: Re: Bug#802321: gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal

[Debian Bug Tracking System]

Processing commands for cont...@bugs.debian.org:

> notfound 802321 gdal/1.11.2+dfsg-3
Bug #802321 [gdal-bin] gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal
No longer marked as found in versions gdal/1.11.2+dfsg-3.
> thanks
Stopping processing here.

Please contact me if you need assistance.
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Bug#802321: marked as done (gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal)

[Debian Bug Tracking System]

Your message dated Tue, 20 Oct 2015 12:19:02 +0200
with message-id <98bb8420244fb94de52601eba6f60...@xs4all.nl>
and subject line Re: Bug#802321: gdal-bin: NetCDF-4 / HDF5 support broken in 
recent gdal
has caused the Debian Bug report #802321,
regarding gdal-bin: NetCDF-4 / HDF5 support broken in recent gdal
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
802321: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=802321
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: gdal-bin
Version: 1.11.2+dfsg-3+b2
Severity: grave
Justification: causes non-serious data loss

NetCDF-4 format is not properly recognized in recent gdal (libgdal1i ?).

How to reproduce the bug: 
--

the attached file JEJK_topoC9k_ZABA10mHbpv.nc  is of NetCDF-4 / HDF5 format, 
see ncdump or h5dump output

$ ncdump -h JEJK_topoC9k_ZABA10mHbpv.nc
netcdf JEJK_topoC9k_ZABA10mHbpv {
dimensions:
x = 501 ;
y = 601 ;
variables:
double x(x) ;
x:long_name = "x" ;
x:actual_range = -546000., -541000. ;
double y(y) ;
y:long_name = "y" ;
y:actual_range = -1073000., -1067000. ;
float z(y, x) ;
z:long_name = "z" ;
z:_FillValue = NaNf ;
z:actual_range = 2.38614749908447, 11.5756139755249 ;

// global attributes:
:Conventions = "COARDS, CF-1.5" ;
:title = "Produced by grdreformat" ;
:history = "grdreformat CRJK_topoC9c_ZABAGED10m.grd 
Jesenik_topoC9_ZABAGED10mBpv.nc -R-546000/-541000/-1073000/-1067000" ;
:GMT_version = "5.1.2 (r14256) [64-bit]" ;
}


$ ncdump -k JEJK_topoC9k_ZABA10mHbpv.nc 
netCDF-4


$ h5dump -n JEJK_topoC9k_ZABA10mHbpv.nc 
HDF5 "JEJK_topoC9k_ZABA10mHbpv.nc" {
FILE_CONTENTS {
 group  /
 dataset/x
 dataset/y
 dataset/z
 }
}




Now see what about gdal:

$ gdalinfo JEJK_topoC9k_ZABA10mHbpv.nc 
ERROR 4: `HDF5:"JEJK_topoC9k_ZABA10mHbpv.nc":z' does not exist in the file 
system,
and is not recognised as a supported dataset name.

gdalinfo failed - unable to open 'JEJK_topoC9k_ZABA10mHbpv.nc'.


The support for NetCDF-4 / HDF-5 output is broken too:

$ gmt grdreformat JEJK_topoC9k_ZABA10mHbpv.grd JEJK_topoC9k_ZABA10mHbpv.xnc=nf
grdreformat (GMTAPI_Export_Grid): NetCDF: HDF error 
[JEJK_topoC9k_ZABA10mHbpv.xnc=nf]
[Session gmt (0)]: Error returned from GMT API: GMT_GRID_WRITE_ERROR (19)


Previous gdal version (1.11.1 perhaps? - in stretch) worked well in this 
respect.

Regards,
Otakar


-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (500, 'testing'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.2.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages gdal-bin depends on:
ii  libc62.19-22
ii  libgcc1  1:5.2.1-22
ii  libgdal1i [libgdal.so.1-1.11.2]  1.11.2+dfsg-3+b2
ii  libstdc++6   5.2.1-22

gdal-bin recommends no packages.

Versions of packages gdal-bin suggests:
ii  python-gdal  1.11.2+dfsg-3+b2

-- no debconf information
--- End Message ---
--- Begin Message ---

notfound 802321 gdal/1.11.2+dfsg-3
thanks

Hi Otakar,

Good to hear that the netcdf package rebuilt for the hdf5 transition 
resolves the issue.


The dependencies generated using the symbols verions generally don't 
include the binNMU version, so we can't easily prevent this kind of 
issue with just dependencies.


This is one of the primary reasons why transitions to new library 
version are coordinated with the release team to have all or most 
packages migrate to testing at the same time.


Kind Regards,

Bas--- End Message ---
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mapnik 3.0.7+ds-4 MIGRATED to testing

[Debian testing watch]

FYI: The status of the mapnik source package
in Debian's testing distribution has changed.

  Previous version: 3.0.5+ds-1
  Current version:  3.0.7+ds-4

-- 
This email is automatically generated once a day.  As the installation of
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later changes on the next day.
See https://release.debian.org/testing-watch/ for more information.

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Bug#802495: pprepair: Fails to build with GDAL 2.0

[Bas Couwenberg]

Source: pprepair
Version: 0.0~20150323-6284890-2
Severity: important
Tags: upstream
User: debian-...@lists.debian.org
Usertags: gdal-2.0

Dear Maintainer,

pprepair (0.0~20150323-6284890-2) FTBFS due to missing compatibility
with GDAL/OGR 2.0:

  error: 'Open' is not a member of 'OGRSFDriverRegistrar'
  error: 'class GDALDriver' has no member named 'GetName'
  error: invalid conversion from 'GDALDriver*' to 'OGRSFDriver*'

The full build log is attached.

pprepair needs to be patched to support GDAL 2.0, please refer to the
'MIGRATION GUIDE FROM GDAL 1.11 to GDAL 2.0' for pointers:

 https://svn.osgeo.org/gdal/branches/2.0/gdal/MIGRATION_GUIDE.TXT

Upstream has no GDAL 2.0 support yet, nor any issue tracking it.

This issue should be forwarded to the pprepair issue tracker on GitHub,
which does not allow attaching build logs.

The severity of this issue will be increased to serious when the GDAL
2.0 transition starts.

There are no GDAL 2.0.1 packages available in experimental yet, because
the transition to GDAL 1.11.3 (#80) needs to start first. This issue
was triaged using locally built GDAL 2.0.1 packages from the
experimental-2.0 branch in git:

 https://anonscm.debian.org/cgit/pkg-grass/gdal.git/log/?h=experimental-2.0

Kind Regards,

Bas
Building with cowbuilder for distribution sid+rebuild
I: using cowbuilder as pbuilder
dpkg-checkbuilddeps: Unmet build dependencies: libcgal-dev
W: Unmet build-dependency in source
dpkg-buildpackage: source package pprepair
dpkg-buildpackage: source version 0.0~20150323-6284890-2
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Bas Couwenberg 
 dpkg-source --before-build pprepair
dpkg-checkbuilddeps: Unmet build dependencies: libcgal-dev
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
dpkg-buildpackage: warning: this is currently a non-fatal warning with -S, but 
will probably become fatal in the future
 fakeroot debian/rules clean
dh clean
   dh_testdir
   dh_auto_clean
   debian/rules override_dh_clean
make[1]: Entering directory '/home/bas/git/pkg-grass/pprepair'
dh_clean debian/man/*.1
make[1]: Leaving directory '/home/bas/git/pkg-grass/pprepair'
 dpkg-source -b pprepair
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building pprepair using existing 
./pprepair_0.0~20150323-6284890.orig.tar.gz
dpkg-source: info: building pprepair in 
pprepair_0.0~20150323-6284890-2.debian.tar.xz
dpkg-source: info: building pprepair in pprepair_0.0~20150323-6284890-2.dsc
 dpkg-genchanges -S >../pprepair_0.0~20150323-6284890-2_source.changes
dpkg-genchanges: not including original source code in upload
 dpkg-source --after-build pprepair
dpkg-buildpackage: binary and diff upload (original source NOT included)
 -> Copying COW directory
  forking: rm -rf /var/cache/pbuilder/build//cow.20273 
  forking: cp -al /var/cache/pbuilder/base-sid+rebuild.cow 
/var/cache/pbuilder/build//cow.20273 
I: removed stale ilistfile /var/cache/pbuilder/build//cow.20273/.ilist
  forking: chroot /var/cache/pbuilder/build//cow.20273 cowdancer-ilistcreate 
/.ilist find . -xdev -path ./home -prune -o \( \( -type l -o -type f \) -a 
-links +1 -print0 \) | xargs -0 stat --format '%d %i ' 
 -> Invoking pbuilder
  forking: pbuilder build --debbuildopts  --debbuildopts  --buildplace 
/var/cache/pbuilder/build//cow.20273 --buildresult /home/bas/git/pkg-grass 
--debbuildopts  --no-targz --internal-chrootexec chroot 
/var/cache/pbuilder/build//cow.20273 cow-shell 
/home/bas/git/pkg-grass/pprepair_0.0~20150323-6284890-2.dsc 
I: Running in no-targz mode
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Oct 20 17:06:12 CEST 2015
I: pbuilder-time-stamp: 1445353572
I: copying local configuration
I: mounting /proc filesystem
I: mounting /run/shm filesystem
I: mounting /dev/pts filesystem
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: Installing the build-deps
W: no hooks of type D found -- ignoring
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team 
Description: Dummy package to satisfy dependencies with aptitude - created by 
pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper (>= 9), cmake, libcgal-dev, libgdal-dev, docbook2x, 
docbook-xsl, docbook-xml, xsltproc
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in 
'/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 12383 files and directories currently installed.)
Preparing to unpack 

Bug#802497: prepair: Fails to build with GDAL 2.0

[Bas Couwenberg]

Source: prepair
Version: 0.7-3
Severity: important
Tags: upstream
User: debian-...@lists.debian.org
Usertags: gdal-2.0

Dear Maintainer,

prepair (0.7-3) FTBFS due to missing compatibility with GDAL/OGR 2.0:

 error: invalid conversion from 'GDALDriver*' to 'OGRSFDriver*'

The full build log is attached.

The full build log is attached.

prepair needs to be patched to support GDAL 2.0, please refer to the
'MIGRATION GUIDE FROM GDAL 1.11 to GDAL 2.0' for pointers:

 https://svn.osgeo.org/gdal/branches/2.0/gdal/MIGRATION_GUIDE.TXT

Upstream has no GDAL 2.0 support yet, nor any issue tracking it.

This issue should be forwarded to the prepair issue tracker on GitHub,
which does not allow attaching build logs.

The severity of this issue will be increased to serious when the GDAL
2.0 transition starts.

There are no GDAL 2.0.1 packages available in experimental yet, because
the transition to GDAL 1.11.3 (#80) needs to start first. This issue
was triaged using locally built GDAL 2.0.1 packages from the
experimental-2.0 branch in git:

 https://anonscm.debian.org/cgit/pkg-grass/gdal.git/log/?h=experimental-2.0

Kind Regards,

Bas
Building with cowbuilder for distribution sid+rebuild
I: using cowbuilder as pbuilder
dpkg-checkbuilddeps: Unmet build dependencies: libcgal-dev
W: Unmet build-dependency in source
dpkg-buildpackage: source package prepair
dpkg-buildpackage: source version 0.7-3
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Bas Couwenberg 
 dpkg-source --before-build prepair
dpkg-source: info: applying readme-example-paths.patch
dpkg-source: info: applying 
0001-Also-list-the-shpOut-option-in-the-usage-information.patch
dpkg-checkbuilddeps: Unmet build dependencies: libcgal-dev
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
dpkg-buildpackage: warning: this is currently a non-fatal warning with -S, but 
will probably become fatal in the future
 fakeroot debian/rules clean
dh clean
   dh_testdir
   dh_auto_clean
   debian/rules override_dh_clean
make[1]: Entering directory '/home/bas/git/pkg-grass/prepair'
dh_clean debian/man/*.1
make[1]: Leaving directory '/home/bas/git/pkg-grass/prepair'
 dpkg-source -b prepair
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building prepair using existing ./prepair_0.7.orig.tar.gz
dpkg-source: info: building prepair in prepair_0.7-3.debian.tar.xz
dpkg-source: info: building prepair in prepair_0.7-3.dsc
 dpkg-genchanges -S >../prepair_0.7-3_source.changes
dpkg-genchanges: not including original source code in upload
 dpkg-source --after-build prepair
dpkg-source: info: unapplying 
0001-Also-list-the-shpOut-option-in-the-usage-information.patch
dpkg-source: info: unapplying readme-example-paths.patch
dpkg-buildpackage: binary and diff upload (original source NOT included)
 -> Copying COW directory
  forking: rm -rf /var/cache/pbuilder/build//cow.18257 
  forking: cp -al /var/cache/pbuilder/base-sid+rebuild.cow 
/var/cache/pbuilder/build//cow.18257 
I: removed stale ilistfile /var/cache/pbuilder/build//cow.18257/.ilist
  forking: chroot /var/cache/pbuilder/build//cow.18257 cowdancer-ilistcreate 
/.ilist find . -xdev -path ./home -prune -o \( \( -type l -o -type f \) -a 
-links +1 -print0 \) | xargs -0 stat --format '%d %i ' 
 -> Invoking pbuilder
  forking: pbuilder build --debbuildopts  --debbuildopts  --buildplace 
/var/cache/pbuilder/build//cow.18257 --buildresult /home/bas/git/pkg-grass 
--debbuildopts  --no-targz --internal-chrootexec chroot 
/var/cache/pbuilder/build//cow.18257 cow-shell 
/home/bas/git/pkg-grass/prepair_0.7-3.dsc 
I: Running in no-targz mode
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Oct 20 17:32:59 CEST 2015
I: pbuilder-time-stamp: 1445355179
I: copying local configuration
I: mounting /proc filesystem
I: mounting /run/shm filesystem
I: mounting /dev/pts filesystem
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: Installing the build-deps
W: no hooks of type D found -- ignoring
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team 
Description: Dummy package to satisfy dependencies with aptitude - created by 
pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper (>= 9), cmake, libcgal-dev, libgdal-dev, docbook2x, 
docbook-xsl, docbook-xml, xsltproc
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in 
'/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 12383 files and directories 

Processed: bug 802497 is forwarded to https://github.com/tudelft3d/prepair/issues/22

[Debian Bug Tracking System]

Processing commands for cont...@bugs.debian.org:

> forwarded 802497 https://github.com/tudelft3d/prepair/issues/22
Bug #802497 [src:prepair] prepair: Fails to build with GDAL 2.0
Set Bug forwarded-to-address to 
'https://github.com/tudelft3d/prepair/issues/22'.
> thanks
Stopping processing here.

Please contact me if you need assistance.
-- 
802497: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=802497
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

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Processed: bug 802495 is forwarded to https://github.com/tudelft3d/pprepair/issues/29

[Debian Bug Tracking System]

Processing commands for cont...@bugs.debian.org:

> forwarded 802495 https://github.com/tudelft3d/pprepair/issues/29
Bug #802495 [src:pprepair] pprepair: Fails to build with GDAL 2.0
Set Bug forwarded-to-address to 
'https://github.com/tudelft3d/pprepair/issues/29'.
> thanks
Stopping processing here.

Please contact me if you need assistance.
-- 
802495: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=802495
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

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