Debian Bug report logs -
#562775
FTBFS: Could not find vtk.jar file, VTK_JAVA_JAR is wrong, please set proper GDCM_VTK_JAVA_JAR replacement var
Reported by: Christoph Egger <christoph@debian.org>
Date: Sun, 27 Dec 2009 20:36:01 UTC
Severity: serious
Found in version vtk/5.2.1-14
Fixed in versions vtk/5.2.1-15, vtk/5.4.2-2, 5.4.2-2
Done: Denis Barbier <bouzim@gmail.com>
Bug is archived. No further changes may be made.
Toggle useless messages
Report forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#562775; Package gdcm.
(Sun, 27 Dec 2009 20:36:04 GMT) (full text, mbox, link).
Acknowledgement sent
to Christoph Egger <christoph@debian.org>:
New Bug report received and forwarded. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Sun, 27 Dec 2009 20:36:04 GMT) (full text, mbox, link).
Message #5 received at submit@bugs.debian.org (full text, mbox, reply):
[Message part 1 (text/plain, inline)]
Package: gdcm
Version: 2.0.14-2
Severity: serious
Justification: fails to build from source
In a clean cowbuilder gdcm fails to build from source on
armel. Excerpt from the buildlog below, the full log attached.
-- Looking for include files HAVE_SYS_TIME_H
-- Looking for include files HAVE_SYS_TIME_H - found
-- Looking for include files HAVE_WINSOCK_H
-- Looking for include files HAVE_WINSOCK_H - not found.
-- Looking for include files HAVE_BYTESWAP_H
-- Looking for include files HAVE_BYTESWAP_H - found
-- Looking for rpc.h
-- Looking for rpc.h - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for _stricmp
-- Looking for _stricmp - not found
-- Looking for _strnicmp
-- Looking for _strnicmp - not found
-- Looking for _snprintf
-- Looking for _snprintf - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
You are using the SWIG version of VTKGDCM. This is not compatible with Activiz
-- Java version 1.6.0.0 configured successfully!
Implicitely adding debian package layout...
CMake Error at Utilities/VTK/CMakeLists.txt:268 (message):
Could not find vtk.jar file, VTK_JAVA_JAR is wrong, please set proper
GDCM_VTK_JAVA_JAR replacement var
-- Configuring incomplete, errors occurred!
make: *** [debian/configure-python2.5-stamp] Error 1
dpkg-buildpackage: error: debian/rules build gave error exit status 2
-- System Information:
Debian Release: squeeze/sid
APT prefers testing
APT policy: (990, 'testing'), (500, 'stable'), (400, 'unstable'), (100, 'experimental')
Architecture: i386 (x86_64)
Kernel: Linux 2.6.31-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
--
/"\ ASCII Ribbon : GPG-Key ID: 0xD49AE731
\ / Campaign : CaCert Assurer
X against HTML : Debian Maintainer
/ \ in eMails : http://www.debian.org/
http://www.christoph-egger.org/
[gdcm_2.0.14-2.dsc.log.realfail (text/plain, attachment)]
[signature.asc (application/pgp-signature, inline)]
Bug reassigned from package 'gdcm' to 'libvtk-java'.
Request was from Mathieu Malaterre <mathieu.malaterre@gmail.com>
to control@bugs.debian.org.
(Mon, 28 Dec 2009 14:42:04 GMT) (full text, mbox, link).
Bug No longer marked as found in versions 2.0.14-2.
Request was from Mathieu Malaterre <mathieu.malaterre@gmail.com>
to control@bugs.debian.org.
(Mon, 28 Dec 2009 14:42:05 GMT) (full text, mbox, link).
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Mon, 28 Dec 2009 16:18:19 GMT) (full text, mbox, link).
Acknowledgement sent
to Mathieu Malaterre <mathieu.malaterre@gmail.com>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Mon, 28 Dec 2009 16:18:19 GMT) (full text, mbox, link).
Message #14 received at 562775@bugs.debian.org (full text, mbox, reply):
On Sun, Dec 27, 2009 at 7:42 PM, Denis Barbier <bouzim@gmail.com> wrote:
> On 2009/12/27 Mathieu Malaterre wrote:
> [...]
>> Does this help ? Even if the path is wrong in VTKConfig.cmake, GDCM
>> can cope with that. In the end /usr/share/java/vtk/vtk.jar should be
>> the vtk jar file.
> [...]
>
> I was confused by your message, /usr/share/java/vtk.jar is the
> expected location of the jar file. and this is what your commit does,
If you do the upload, please close this new bug too. thanks
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=562775
--
Mathieu
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Sat, 02 Jan 2010 07:03:04 GMT) (full text, mbox, link).
Acknowledgement sent
to Dominique Belhachemi <domibel@cs.tu-berlin.de>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Sat, 02 Jan 2010 07:03:04 GMT) (full text, mbox, link).
Message #19 received at 562775@bugs.debian.org (full text, mbox, reply):
Hi Mathieu,
You are right. Using /usr/share/java/vtk/vtk.jar solves the problem.
BTW, I was playing with vtk-5.4 in experimental and tried to compile
gdcm. There is another java related problem. I was getting an error
message. Here it is:
-------------------------------------------------------
Linking CXX shared library ../../bin/libvtkgdcmJava.so
/usr/bin/ld: error: cannot find -lvtkCommonJava
/usr/bin/ld: error: cannot find -lvtkIOJava
/usr/bin/ld: error: cannot find -lvtkImagingJava
/usr/bin/ld: error: cannot find -lvtkRenderingJava
/usr/bin/ld: error: cannot find -lvtkImagingJava
/usr/bin/ld: error: cannot find -lvtkGraphicsJava
/usr/bin/ld: error: cannot find -lvtkFilteringJava
/usr/bin/ld: error: cannot find -lvtkCommonJava
collect2: ld returned 1 exit status
make[3]: *** [bin/libvtkgdcmJava.so] Error 1
-------------------------------------------------------
Those libraries have been located in /usr/lib/ .
Since a while they are located in /usr/lib/jni/ .
Following patch helps in my case:
-------------------------------------------------------------------
--- gdcm-2.0.14.orig/Utilities/VTK/CMakeLists.txt
+++ gdcm-2.0.14/Utilities/VTK/CMakeLists.txt
@@ -242,17 +242,16 @@
INCLUDE(${VTK_CMAKE_DIR}/vtkWrapJava.cmake)
INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
+ if(EXISTS /usr/lib/jni/libvtkCommonJava.so)
+ message("Implicitely adding debian package layout...")
+ link_directories("/usr/lib/jni")
+ endif()
+
VTK_WRAP_JAVA3(${VTKGDCM_NAME}Java vtkgdcmJAVA_SRCS
"${vtkgdcm_SRCS}")
# libvtk-java is a pain to handle...
if(EXISTS ${VTK_JAVA_JAR})
# http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533193
set(GDCM_VTK_JAVA_JAR ${VTK_JAVA_JAR})
- else(EXISTS ${VTK_JAVA_JAR})
- # http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533198
- if(EXISTS /usr/lib/jni/libvtkCommonJava.so)
- message("Implicitely adding debian package layout...")
- link_directories("/usr/lib/jni")
- endif()
endif(EXISTS ${VTK_JAVA_JAR})
MARK_AS_ADVANCED(GDCM_VTK_JAVA_JAR)
if(EXISTS ${GDCM_VTK_JAVA_JAR})
-------------------------------------------------------------------
Cheers
Dominique
On Mon, 2009-12-28 at 17:17 +0100, Mathieu Malaterre wrote:
> On Sun, Dec 27, 2009 at 7:42 PM, Denis Barbier <bouzim@gmail.com> wrote:
> > On 2009/12/27 Mathieu Malaterre wrote:
> > [...]
> >> Does this help ? Even if the path is wrong in VTKConfig.cmake, GDCM
> >> can cope with that. In the end /usr/share/java/vtk/vtk.jar should be
> >> the vtk jar file.
> > [...]
> >
> > I was confused by your message, /usr/share/java/vtk.jar is the
> > expected location of the jar file. and this is what your commit does,
>
> If you do the upload, please close this new bug too. thanks
>
> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=562775
>
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Sat, 02 Jan 2010 23:27:08 GMT) (full text, mbox, link).
Acknowledgement sent
to Denis Barbier <bouzim@gmail.com>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Sat, 02 Jan 2010 23:27:08 GMT) (full text, mbox, link).
Message #24 received at 562775@bugs.debian.org (full text, mbox, reply):
On 2010/1/2 Dominique Belhachemi wrote:
> Hi Mathieu,
>
> You are right. Using /usr/share/java/vtk/vtk.jar solves the problem.
>
> BTW, I was playing with vtk-5.4 in experimental and tried to compile
> gdcm. There is another java related problem.
[...]
Be warned that libvtk-java from experimental is also screwed up,
vtk.jar is absent from this package. This is due to commit 6f4a938,
it should have been reverted in b3e7451. It has now been fixed in
git.
Denis
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Sun, 03 Jan 2010 14:48:09 GMT) (full text, mbox, link).
Acknowledgement sent
to Mathieu Malaterre <mathieu.malaterre@gmail.com>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Sun, 03 Jan 2010 14:48:09 GMT) (full text, mbox, link).
Message #29 received at 562775@bugs.debian.org (full text, mbox, reply):
Could someone please let me know what is going on ?
http://packages.debian.org/search?suite=experimental&arch=any&mode=path&searchon=contents&keywords=vtk.jar
Where is vtk.jar ?
Dominique, I am not sure I understand your patch. Until I see a
correct libvtk-java package I do not think I need to patch anything in
GDCM.
Thanks.
On Sat, Jan 2, 2010 at 7:52 AM, Dominique Belhachemi
<domibel@cs.tu-berlin.de> wrote:
> Hi Mathieu,
>
> You are right. Using /usr/share/java/vtk/vtk.jar solves the problem.
>
> BTW, I was playing with vtk-5.4 in experimental and tried to compile
> gdcm. There is another java related problem. I was getting an error
> message. Here it is:
> -------------------------------------------------------
> Linking CXX shared library ../../bin/libvtkgdcmJava.so
> /usr/bin/ld: error: cannot find -lvtkCommonJava
> /usr/bin/ld: error: cannot find -lvtkIOJava
> /usr/bin/ld: error: cannot find -lvtkImagingJava
> /usr/bin/ld: error: cannot find -lvtkRenderingJava
> /usr/bin/ld: error: cannot find -lvtkImagingJava
> /usr/bin/ld: error: cannot find -lvtkGraphicsJava
> /usr/bin/ld: error: cannot find -lvtkFilteringJava
> /usr/bin/ld: error: cannot find -lvtkCommonJava
> collect2: ld returned 1 exit status
> make[3]: *** [bin/libvtkgdcmJava.so] Error 1
> -------------------------------------------------------
>
> Those libraries have been located in /usr/lib/ .
> Since a while they are located in /usr/lib/jni/ .
>
> Following patch helps in my case:
>
> -------------------------------------------------------------------
> --- gdcm-2.0.14.orig/Utilities/VTK/CMakeLists.txt
> +++ gdcm-2.0.14/Utilities/VTK/CMakeLists.txt
> @@ -242,17 +242,16 @@
> INCLUDE(${VTK_CMAKE_DIR}/vtkWrapJava.cmake)
> INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
>
> + if(EXISTS /usr/lib/jni/libvtkCommonJava.so)
> + message("Implicitely adding debian package layout...")
> + link_directories("/usr/lib/jni")
> + endif()
> +
> VTK_WRAP_JAVA3(${VTKGDCM_NAME}Java vtkgdcmJAVA_SRCS
> "${vtkgdcm_SRCS}")
> # libvtk-java is a pain to handle...
> if(EXISTS ${VTK_JAVA_JAR})
> # http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533193
> set(GDCM_VTK_JAVA_JAR ${VTK_JAVA_JAR})
> - else(EXISTS ${VTK_JAVA_JAR})
> - # http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533198
> - if(EXISTS /usr/lib/jni/libvtkCommonJava.so)
> - message("Implicitely adding debian package layout...")
> - link_directories("/usr/lib/jni")
> - endif()
> endif(EXISTS ${VTK_JAVA_JAR})
> MARK_AS_ADVANCED(GDCM_VTK_JAVA_JAR)
> if(EXISTS ${GDCM_VTK_JAVA_JAR})
> -------------------------------------------------------------------
>
> Cheers
> Dominique
>
>
>
>
>
> On Mon, 2009-12-28 at 17:17 +0100, Mathieu Malaterre wrote:
>> On Sun, Dec 27, 2009 at 7:42 PM, Denis Barbier <bouzim@gmail.com> wrote:
>> > On 2009/12/27 Mathieu Malaterre wrote:
>> > [...]
>> >> Does this help ? Even if the path is wrong in VTKConfig.cmake, GDCM
>> >> can cope with that. In the end /usr/share/java/vtk/vtk.jar should be
>> >> the vtk jar file.
>> > [...]
>> >
>> > I was confused by your message, /usr/share/java/vtk.jar is the
>> > expected location of the jar file. and this is what your commit does,
>>
>> If you do the upload, please close this new bug too. thanks
>>
>> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=562775
>>
>
>
>
--
Mathieu
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Sun, 03 Jan 2010 23:48:06 GMT) (full text, mbox, link).
Acknowledgement sent
to Denis Barbier <bouzim@gmail.com>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Sun, 03 Jan 2010 23:48:06 GMT) (full text, mbox, link).
Message #34 received at 562775@bugs.debian.org (full text, mbox, reply):
On 2010/1/3 Mathieu Malaterre wrote:
> Could someone please let me know what is going on ?
>
> http://packages.debian.org/search?suite=experimental&arch=any&mode=path&searchon=contents&keywords=vtk.jar
>
> Where is vtk.jar ?
Hi Mathieu,
As explained in a previous mail, it had accidentally been dropped from
libvtk-java. Dominique uploaded 5.4.2-2 to fix this issue.
> Dominique, I am not sure I understand your patch. Until I see a
> correct libvtk-java package I do not think I need to patch anything in
> GDCM.
Dominique is right, when vtk.jar is found, you do no more pass into the
else(EXISTS ${VTK_JAVA_JAR})
branch and libraries in /usr/lib/jni are not found.
But maybe it would be better to set a variable in VTKConfig.cmake to
let VTK tell where it puts JNI libraries?
There are other problems, you asked to enable more VTK_USE_* features,
and as a consequence more dependencies have been defined in
/usr/lib/vtk-5.4/VTKLibraryDepends.cmake, libvtk5-dev must depend on
all the .so libraries listed there (except for the wrappings).
Hopefully this is now fixed in the git repository.
Denis
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Mon, 04 Jan 2010 10:27:04 GMT) (full text, mbox, link).
Acknowledgement sent
to Mathieu Malaterre <mathieu.malaterre@gmail.com>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Mon, 04 Jan 2010 10:27:04 GMT) (full text, mbox, link).
Message #39 received at 562775@bugs.debian.org (full text, mbox, reply):
Denis,
On Mon, Jan 4, 2010 at 12:44 AM, Denis Barbier <bouzim@gmail.com> wrote:
> On 2010/1/3 Mathieu Malaterre wrote:
>> Could someone please let me know what is going on ?
>>
>> http://packages.debian.org/search?suite=experimental&arch=any&mode=path&searchon=contents&keywords=vtk.jar
>>
>> Where is vtk.jar ?
>
> Hi Mathieu,
>
> As explained in a previous mail, it had accidentally been dropped from
> libvtk-java. Dominique uploaded 5.4.2-2 to fix this issue.
I think this upload did not fix this particular issue:
http://packages.debian.org/experimental/i386/libvtk-java/filelist
>> Dominique, I am not sure I understand your patch. Until I see a
>> correct libvtk-java package I do not think I need to patch anything in
>> GDCM.
>
> Dominique is right, when vtk.jar is found, you do no more pass into the
> else(EXISTS ${VTK_JAVA_JAR})
> branch and libraries in /usr/lib/jni are not found.
I see. Thanks !
> But maybe it would be better to set a variable in VTKConfig.cmake to
> let VTK tell where it puts JNI libraries?
Technically this is the best solution.
> There are other problems, you asked to enable more VTK_USE_* features,
> and as a consequence more dependencies have been defined in
> /usr/lib/vtk-5.4/VTKLibraryDepends.cmake, libvtk5-dev must depend on
> all the .so libraries listed there (except for the wrappings).
> Hopefully this is now fixed in the git repository.
Cool !
--
Mathieu
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Mon, 04 Jan 2010 10:33:11 GMT) (full text, mbox, link).
Acknowledgement sent
to Denis Barbier <bouzim@gmail.com>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Mon, 04 Jan 2010 10:33:11 GMT) (full text, mbox, link).
Message #44 received at 562775@bugs.debian.org (full text, mbox, reply):
On 2010/1/4 Mathieu Malaterre wrote:
[...]
>> As explained in a previous mail, it had accidentally been dropped from
>> libvtk-java. Dominique uploaded 5.4.2-2 to fix this issue.
>
> I think this upload did not fix this particular issue:
>
> http://packages.debian.org/experimental/i386/libvtk-java/filelist
Mathieu,
I do not know why, but this page is wrong; if you download the i386
package, you will see that vtk.jar is present.
Denis
Information forwarded
to debian-bugs-dist@lists.debian.org, bottoms@debian.org (A. Maitland Bottoms):
Bug#562775; Package libvtk-java.
(Mon, 04 Jan 2010 11:27:10 GMT) (full text, mbox, link).
Acknowledgement sent
to Mathieu Malaterre <mathieu.malaterre@gmail.com>:
Extra info received and forwarded to list. Copy sent to bottoms@debian.org (A. Maitland Bottoms).
(Mon, 04 Jan 2010 11:27:10 GMT) (full text, mbox, link).
Message #49 received at 562775@bugs.debian.org (full text, mbox, reply):
On Mon, Jan 4, 2010 at 11:31 AM, Denis Barbier <bouzim@gmail.com> wrote:
> On 2010/1/4 Mathieu Malaterre wrote:
> [...]
>>> As explained in a previous mail, it had accidentally been dropped from
>>> libvtk-java. Dominique uploaded 5.4.2-2 to fix this issue.
>>
>> I think this upload did not fix this particular issue:
>>
>> http://packages.debian.org/experimental/i386/libvtk-java/filelist
>
> Mathieu,
>
> I do not know why, but this page is wrong; if you download the i386
> package, you will see that vtk.jar is present.
Much better !
So what is the next step, there are two working vtk AFAIK:
- 5.4.2-2
- 5.2.1-11
Dominique, could you please push 5.4.2-2 to unstable ? Will there be
a mechanism to force a rebuild of any rdepend package (since ABI
changed) ?
Thanks
--
Mathieu
Added indication that bug 562775 blocks 564246
Request was from Mathieu Malaterre <mathieu.malaterre@gmail.com>
to control@bugs.debian.org.
(Tue, 12 Jan 2010 09:33:13 GMT) (full text, mbox, link).
Bug Marked as found in versions vtk/5.2.1-14.
Request was from Denis Barbier <bouzim@gmail.com>
to control@bugs.debian.org.
(Tue, 26 Jan 2010 10:24:06 GMT) (full text, mbox, link).
Bug Marked as fixed in versions vtk/5.2.1-15.
Request was from Denis Barbier <bouzim@gmail.com>
to control@bugs.debian.org.
(Tue, 26 Jan 2010 10:24:07 GMT) (full text, mbox, link).
Bug Marked as fixed in versions vtk/5.4.2-2.
Request was from Denis Barbier <bouzim@gmail.com>
to control@bugs.debian.org.
(Tue, 26 Jan 2010 10:24:07 GMT) (full text, mbox, link).
Reply sent
to Denis Barbier <bouzim@gmail.com>:
You have taken responsibility.
(Wed, 27 Jan 2010 11:21:09 GMT) (full text, mbox, link).
Notification sent
to Christoph Egger <christoph@debian.org>:
Bug acknowledged by developer.
(Wed, 27 Jan 2010 11:21:09 GMT) (full text, mbox, link).
Message #62 received at 562775-done@bugs.debian.org (full text, mbox, reply):
Version: 5.4.2-2
This bug has been fixed in VTK 5.4.2-2, closing it now.
Denis
Bug archived.
Request was from Debbugs Internal Request <owner@bugs.debian.org>
to internal_control@bugs.debian.org.
(Thu, 06 May 2010 08:08:45 GMT) (full text, mbox, link).
Send a report that this bug log contains spam.
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