Re: [Debian-med-packaging] Bug#753809: Bug#753809: ginkgocadx, orthanc and sending/receiving data
Hi, On 03.03.2016 16:30, Gert Wollny wrote: > [everything looks fine except image transfer] It seems that either I > introduced some regression when I ported the code - although I > barely touched the DCMTK related part - I only changed some constant > names, or dcmtk-3.6.1 changed this part with respect to dcmtk-3.6.0 > (the version used by the pre-compiled ginkgocadx), and I would need > to adjust the parameters of the corresponding DIMSE call. I don't think we made serious changes in DCMTK's networking code, instead, we really try hard to keep it backward compatible (if we change something at all). I mean you could try 3.6.0 source code just for checking its not a DCMTK issue, if it still compiles on a current sytem (it's already some years old...). Also, if its easily possible in the source code, try to set a more detailed DCMTK log level [1] Best, Michael [1] http://support.dcmtk.org/redmine/projects/dcmtk/wiki/Howto_LogProgram
Re: [Debian-med-packaging] Bug#753809: Bug#753809: ginkgocadx, orthanc and sending/receiving data
Thanks for the insight! > So my guess is the following: > > -Either the AE title that should receive the images is not configured > with IP and port on the server. It should be configured correctly, because when I run the downloadable pre-compiled version of Ginkgocadx, it uses the same configuration files, and the MOVE operation works. > -Or there is such an AE title's IP and port configured (or even > guessed by the server) but no one is listening at that address. Well, I can do telnet localhost 2 and get the standard answer Trying 127.0.0.1 Connected to localhost Escape character is ... and the GinkgoCADx side says D: setting network send timeout to 60 seconds D: setting network receive timeout to 60 seconds E: Receiving Association failed: 0006:031a DUL network read timeout Which means the port is open, and listening. It seems that either I introduced some regression when I ported the code - although I barely touched the DCMTK related part - I only changed some constant names, or dcmtk-3.6.1 changed this part with respect to dcmtk-3.6.0 (the version used by the pre-compiled ginkgocadx), and I would need to adjust the parameters of the corresponding DIMSE call. Best, Gert
Re: [Debian-med-packaging] Bug#753809: ginkgocadx, orthanc and sending/receiving data
Hi,
On 02.03.2016 16:05, Gert Wollny wrote:
> https://orthanc.chu.ulg.ac.be/book/faq/query-retrieve.html
>
> This was helpful indeed, now I find the data, but downloading fails.
>
> With the MOVE method GinkgoCADx says (after some time):
> [...]
> and Orthanc logs:
>
> W0302 14:08:55.689193 OrthancMoveRequestHandler.cpp:171] Move-SCU
> request received for AET "GINKGO"
> E0302 14:09:55.837689 DicomUserConnection.cpp:159]
> DicomUserConnection: Peer aborted Association (or never connected)
The client tells the server via "MOVE" to send the images. However, MOVE
is a 3 point protocol: The client tells the server in the MOVE request
which images to send but also, to which AE title (i.e. which DICOM node
on the network) they should be send. This can be the client's own AE
Title (i.e. a listener under its control) or any other system. Thus, the
images are always(!) sent on a different DICOM connection than the
original MOVE request and those connections are between the same two
systems or three systems.
Since the client does only tell the server the move destination (as the
target system is called) via the AE Title and does not provide IP
address and port, those two have to be configured on the server for each
AE Title that should be able to receive images being requested via MOVE.
So my guess is the following:
- Either the AE title that should receive the images is not configured
with IP and port on the server.
- Or there is such an AE title's IP and port configured (or even guessed
by the server) but no one is listening at that address.
The latter seems to be more likely since the server seems to run into a
timeout while trying to connect to the storage destination. Also for the
former there should be a particular error code "Move Destination
Unknown" which should be returned by the server to the MOVE client.
Probably Karsten can give more insights of the move destination
configuration.
> E0302 14:09:55.837942 MoveScp.cpp:183] IMoveRequestHandler Failed:
> Error in the network protocol
>
> With the GET method, ginkgocadx rejects the request immediately:
>
> E: Error Downloading study: Exception in component GIL/PACS : E:
> DIMSE No valid Presentation Context ID
This means (without seeing the full negotiation logs) that the server
does not support download via "GET", i.e. the related "SOP Class" could
not be negotiated. Overall, not any of the service proposals
("Presentation Contexts") of the request could be accepted by the server
(probably since the client just asks for the GET-related service(s)).
GET is not as common as MOVE as a download method so that is not really
unexpected behaviour. One reason is that GET always downloads on the
same connection, i.e. you only can request the images for yourself and
cannot send them a third system. On the other hand, with GET you never
run into firewall troubles and you do not have to pre-configure image
storage destination AE Titles on the server but you can download right away.
HTH,
Michael
P.S: Some time ago I wrote a "short" introduction/troubleshooting to
DICOM networking with DCMTK which covers many of the issues described.
Maybe its helpful for one the readers.
http://support.dcmtk.org/redmine/projects/dcmtk/wiki/Howto_PACSDebuggingWithDCMTK
Re: ginkgocadx, orthanc and sending/receiving data
On Wed, Mar 02, 2016 at 12:28:41PM +0100, Gert Wollny wrote: > I've installed the Orthanc server and successfully send some data to > the server. ... > Retrieving the data was unsuccessful, because Orthanc tells me > > W0302 10:43:16.730446 main.cpp:630] Orthanc has started > E0302 10:47:10.008827 main.cpp:182] Unknown remote DICOM modality AET: > "GINKGO_001" > E0302 10:47:10.008896 CommandDispatcher.cpp:781] Find requests are > disallowed for the AET "GINKGO_001" ... > To me quiet surprising, since I was able to send the data. I don't know everything about DICOM but this may be the rationale: In the DICOM world the AET (Application Entity Title) is used as a crude authentication scheme where the AET is sort of an account without a password. In short, it seems that when a DICOM client tells a DICOM server: "Hey, I am $AET!" the server will look up its list of known friends and - if found - gladly send out data. Now, since *uploading* data means the client has got the data _already_ there is no privacy leak as far as Orthanc is concerned, hence sending succeeds even without this AET being defined inside Orthanc. In order to get Orthanc to send data to Ginkgo CADx, which (configurably) tries to connect under the name "GINKGO_001" (see Orthanc log) we will have to tell Orthanc: "Yep, GINKGO_001 is a legit client." This is done by modifying =/etc/orthanc/orthanc.json=, more specifically, the section about "DicomModalities". Within that part you'll have to create a line like this: "GINKGO_001" : [ "GINKGO_001", "127.0.0.1", 4243 ] below the "clearcanvas : [...]" line. Note the 424-THREE in there - this is the port that Gingko CADx is _listening_ to replies from Orthanc, which - itself - is listening on port 4242 to request _from_ Ginkgo. You will have to set this 4243 port somehwere in the client configuration of Ginkgo CADx as well. I don't know the exact window/field for it off the top of my head. Also see #5 under http://ginkgo-cadx.com/en/ Karsten -- GPG key ID E4071346 @ eu.pool.sks-keyservers.net E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346
ginkgocadx -> experimental
Hello all, I've just uploaded an updated version of ginkgocadx to experimental. It is known to crash on exit [1], and at this point I'm not sure how to fix this. Also, the main window is always maximized, and if one closes the main window while the history is still open, it may happen that the application doesn't exit. For the bold who want to test it, it should be possible to run it on a sid installation, and if you have an account on GitHub, please report bugs directly there. Unfortunately, doing a statically linked version is quite difficult, because this would need to compile at least also VTK and ITK statically, since they don't provide static libraries on Debian. Hence, I didn't do this right now. Best, Gert
Re: ginkgocadx ...The good, the bad, and the ugly
Hi, just wanted to give you the heads up on how this goes: The good: I got it to build and it runs, thumbnails now work, and also the loading of the borked dicom file (thanks to Matheu's patch for GDCM). The bad: This was all done on Gentoo, because the current versions of VTK and GDCM don't cut it: * VTK < 6.2.1 has a bug that makes ginkgocadx crash when creating the thumbnails. * GDCM-2.6.3 + patch can't currently be build in a clean unstable, because the build dependencies pull in conflicting versions of libopenmpi (1.6 and 1.10). The ugly: The ginkgocadx code is a mess, threading is poorly implemented with the result that at exit the program either crashes or hangs. Luckily gcc now implements a thread-checker that gives some hints what is going wrong, but resolving this threading issue will still be difficult. -- This means we'll have to wait until the gdcm can be build again, and I'll ask the VTK maintainer what he think about uploading either vtk -6.2.1, or vtk-6.3. vtk-7.0 is just around the corner, and both (vtk -6.3 and vtk-7.0) will need to pass through NEW ... Best, Gert
Re: ginkgocadx ...
Hi Gert,
On 29.01.2016 14:41, Gert Wollny wrote:
>> let me know what kind of problems you encountered.
>
> Nice, here they are:
>
> (1) UID_FINDGeneralPurposeWorklistInformationModel is gone (no
> changelog entry though)
This is an easy one (if you know where to look:). From time to time
DICOM removes ("retires") services from the standard that have
never/rarely been implemented in practice. Sometimes alternative
services are available, in this case one could use the "Unified Worklist
and Procedure Step" service.
Long story short: The UID constant has been renamed to
UID_RETIRED_FINDGeneralPurposeWorklistInformationModel which is the one
to use. We do the same for other retired services.
> My workaround: I defined it to its old value
> "1.2.840.10008.5.1.4.32.1" in the source file where it was used.
Clean solution from the functional point of view.
> [oflog stuff]
No idea about those yet since I do not know much about unicode or the
log4cplus integration in DCMTK (someone else did that some time ago, and
we also should upgrade our copy).
> i.e. I defined:
>
> #define DCMTK_LOG4CPLUS_TRACELOGGER_H #define
> DCMTK_LOG4CPLUS_LOGGING_MACROS_HEADER_
>
> Then I prayed for forgiveness and all compiled and linked.
If they are not used (as you said) this sounds like a viable solution...
I cannot offer other insights, sorry.
> I'd be grateful for any help, be advised though, that the developers
> of ginkgocadx did a lot of dirty coding, e.g. copying files from
> original libraries and then slightly adjusting them. For example
> they provided a copy of offile.h with their own changed
> implementation of OFFile without changing the class name or the
> header guard define.
>
> That means it is quite possibe that this last error is a result of
> such a mixup and the only way to find this is digging through the
> preprocessed source.
I tend to believe the same.
If you encounter something that looks wrong on the DCMTK side of things
do not hesitate to contact me again, we also can patch upstream DCMTK if
it makes sense.
> ... but first I have to fix the VTK transition bugs.
Best regards,
Michael
Re: ginkgocadx ...
Hello Michael,
> As one of the DCMTK developers I maybe can help (or contact the
> adequate person of the DCMTK team), so let me know what kind of
> problems you encountered.
Nice, here they are:
(1)
UID_FINDGeneralPurposeWorklistInformationModel is gone (no changelog
entry though)
My workaround: I defined it to its old value "1.2.840.10008.5.1.4.32.1"
in the source file where it was used.
(2)
The original code had
LOG4CPLUS_BEGIN_SYNCHRONIZE_ON_MUTEX( getLogLog().mutex )
...
LOG4CPLUS_END_SYNCHRONIZE_ON_MUTEX;
After adding the DCMTK_ prefix it turned out that the mutex is now private:
ERROR: <<<<
In file included from
/home/gerddie/src/External/ginkgocadx-3.7.1.1573.41/src/cadxcore/main/controllers/log4cplus/guiappender.cpp:15:0:
/usr/include/dcmtk/oflog/helpers/loglog.h: In member function ‘virtual void
gnkLog4cplus::GUIAppender::append(const
dcmtk::log4cplus::spi::InternalLoggingEvent&)’:
/usr/include/dcmtk/oflog/helpers/loglog.h:132:27: error:
‘dcmtk::log4cplus::thread::Mutex dcmtk::log4cplus::helpers::LogLog::mutex’ is
private
thread::Mutex mutex;
^
/home/gerddie/src/External/ginkgocadx-3.7.1.1573.41/src/cadxcore/main/controllers/log4cplus/guiappender.cpp:116:58:
error: within this context
DCMTK_LOG4CPLUS_BEGIN_SYNCHRONIZE_ON_MUTEX( getLogLog().mutex )
>>>>
I removed the locking calls in the hope that somehow whatever needs to be
locked there is now locked inside the logger class, I now get some
async-X-errors when exiting the application.
It seems though, that is this case the original developers mis-used this mutex
to also handle the access to their GUI-based log, so I guess this is something
that I would have to correct independently of DCMTK.
(3) (This is the big one)
For some reason dcmtk-3.6.1-20150924 has an hiccup in
dcmth/oflog/ logger.h and logmacro.h that is related to UNICODE:
ERROR<<<<
In file included from /usr/include/dcmtk/oflog/logmacro.h:37:0,
from /usr/include/dcmtk/oflog/oflog.h:29,
from /usr/include/dcmtk/dcmdata/dctypes.h:27,
from /usr/include/dcmtk/dcmdata/dctk.h:28,
from /home/gerddie/src/External/ginkgocadx
-3.7.1.1573.41/src/cadxcore/main/controllers/dcmtk/libi2d/d2dcommon.h:5
,
from /home/gerddie/src/External/ginkgocadx
-3.7.1.1573.41/src/cadxcore/main/controllers/dcmtk/libi2d/document2dcm.
h:28,
from /home/gerddie/src/External/ginkgocadx
-3.7.1.1573.41/src/cadxcore/main/controllers/dcmtk/dicomimg2dcm.cpp:38:
/usr/include/dcmtk/oflog/tracelog.h: In constructor
‘dcmtk::log4cplus::TraceLogger::TraceLogger(const
dcmtk::log4cplus::Logger&, const tstring&, const char*, int)’:
/usr/include/dcmtk/oflog/tracelog.h:59:79: error: invalid conversion
from ‘const wchar_t*’ to ‘char’ [-fpermissive]
logger.forcedLog(TRACE_LOG_LEVEL,
DCMTK_LOG4CPLUS_TEXT("ENTER: ") + msg, file, line);
>>>>>
Later on I get:
ERROR: <<<<
In file included from /usr/include/dcmtk/oflog/oflog.h:28:0,
from /usr/include/dcmtk/dcmdata/dctypes.h:27,
from /usr/include/dcmtk/dcmdata/dctk.h:28,
from /home/gerddie/src/External/ginkgocadx
-3.7.1.1573.41/src/cadxcore/main/controllers/dcmtk/libi2d/d2dcommon.h:5
,
from /home/gerddie/src/External/ginkgocadx
-3.7.1.1573.41/src/cadxcore/main/controllers/dcmtk/libi2d/document2dcm.
h:28,
from /home/gerddie/src/External/ginkgocadx
-3.7.1.1573.41/src/cadxcore/main/controllers/dcmtk/dicomimg2dcm.cpp:38:
/usr/include/dcmtk/oflog/logger.h:112:23: note: candidate: static
dcmtk::log4cplus::Logger dcmtk::log4cplus::Logger::getInstance(const
tstring&)
static Logger getInstance(const log4cplus::tstring& name);
^
/usr/include/dcmtk/oflog/logger.h:112:23: note: no known conversion
for argument 1 from ‘const tchar* {aka const wchar_t*}’ to ‘const
tstring& {aka const OFString&}’
/usr/include/dcmtk/oflog/logger.h:126:23: note: candidate: static
dcmtk::log4cplus::Logger dcmtk::log4cplus::Logger::getInstance(const
tstring&, dcmtk::log4cplus::spi::LoggerFactory&)
static Logger getInstance(const log4cplus::tstring& name,
spi::LoggerFactory& factory);
>>>>
I tried to define UNICODE at the compile command line, I tried moving
the includes up so that wxWidgets doesn't provide defines that may mix
up the code, but to no avail:
Finally, since these loggers are not used, I defined the include guards
before including anything from dcmtk to avoid that these files are read
at all, i.e. I defined:
#define DCMTK_LOG4CPLUS_TRACELOGGER_H
#define DCMTK_LOG4CPLUS_LOGGING_MACROS_HEADER_
Then I prayed for forgiveness and all compiled and linked.
I'd be grateful for any help, be advised though, that the developers of
ginkgocadx did a lot of dir
Re: ginkgocadx ...
Hi Gert, On Fri, Jan 29, 2016 at 01:04:58PM +0100, Gert Wollny wrote: > > > What is your source of information that says upstream is no more? To the best of my knowledge upstream stopped the *free* flavour of the code. I think there was some discussion here on the list - Karsten might know better. Kind regards Andreas. -- http://fam-tille.de
Re: ginkgocadx ...
On Thu, Jan 28, 2016 at 11:12:00PM +0100, Gert Wollny wrote: > now that I tested the application a bit, I notes that my changes result > in exceptions in thumbnail creation and some Xfree error when exiting. > > Both things are very likely related to my changes, and I will see if I > can fix them before doing the upload. Thanks for working on this. Karsten -- GPG key ID E4071346 @ eu.pool.sks-keyservers.net E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346
Re: ginkgocadx ...
Hi Karsten, On Thu, 2016-01-28 at 21:27 +0100, Karsten Hilbert wrote: [...] > and upstream is no more. > What is your source of information that says upstream is no more? On the Gonkgo CADX web page [1], the at least update the page copyright year to 2016, and on the sourceforge projects page [2], the last activity is recorded to be on 2015-11-16. My point is, if the code is really abandoned by upstream, then I would fork it, put a copy on github, and update it there. The patches I'm working on are quite big, and with quilt one can do only so much. With a public VCS repo other people might feel feel inclined to join in maintaining the code. Best, Gert [1] http://ginkgo-cadx.com/en/ [2] http://sourceforge.net/u/diegogm/profile/
Re: ginkgocadx ...
On Thu, Jan 28, 2016 at 09:03:47PM +0100, Andreas Tille wrote: > > I didn't upload a new version, because I have no rights, > > I felt competent to fix at least this. ;-) > > > but also > > because it would be best if this test of functionality would be done > > first. > > Uploading to experimental might be an option. I would assume Karsten > is keen on testing your work. I can't unless I can get a statically compiled version because I cannot upgrade my Testing. Any suggestions ? However, upstream is dead. So that's that. Karsten -- GPG key ID E4071346 @ eu.pool.sks-keyservers.net E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346
Re: ginkgocadx ...
Hello, now that I tested the application a bit, I notes that my changes result in exceptions in thumbnail creation and some Xfree error when exiting. Both things are very likely related to my changes, and I will see if I can fix them before doing the upload. On Thu, 2016-01-28 at 21:27 +0100, Karsten Hilbert wrote: > On Thu, Jan 28, 2016 at 08:54:50PM +0100, Gert Wollny wrote: > Unfortunately, it currently doesn't do what it is supposed to > (there's a bug) and upstream is no more. I also had a look at that bug report [1], and I think I found the culprit, I'm not sure how to quell this right now, but I'll see what I can do. At least I should be able to give Matheu some better bug report. Best, Gert [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=753809
ginkgocadx ...
Hi all, I've updated the ginkgocadx package to make it compile with VTK6 and DCMTK-3.6.1-20150924. There are some problems, however: Some of the changes for the VTK6 transition are guess-work, and since I have no idea what the program is actually supposed to do, I can not test whether the changes I applied do not change the way the program is supposed to work. Likewise with DCMTK, I had to use some dirty tricks to get everything compile, i.e. there seems to be a problem with UNICODE and DCMTK, and one Dicom UID no longer exists or was renamed. Which means, if there is someone amongst you who actually knows the program, it would be nice if you could test whether it still behaves correctly. I didn't upload a new version, because I have no rights, but also because it would be best if this test of functionality would be done first. Best, Gert
Re: ginkgocadx ...
On Thu, Jan 28, 2016 at 08:54:50PM +0100, Gert Wollny wrote: > > I didn't upload a new version, because I have no rights, I felt competent to fix at least this. ;-) > but also > because it would be best if this test of functionality would be done > first. Uploading to experimental might be an option. I would assume Karsten is keen on testing your work. Thanks a lot for working on these long standing issues which is very appreciated Andreas. -- http://fam-tille.de
Re: ginkgocadx ...
Am Thursday 28 January 2016, 21:03:47 schrieb Andreas Tille: > On Thu, Jan 28, 2016 at 08:54:50PM +0100, Gert Wollny wrote: > > I didn't upload a new version, because I have no rights, > > I felt competent to fix at least this. ;-) > > > but also > > because it would be best if this test of functionality would be done > > first. > > Uploading to experimental might be an option. I would assume Karsten > is keen on testing your work. I am not sure where Ginkgocadx is headed. Latest release seems to be a bit dated. There used to be a forum but I cannot find it anymore. There was a Pro version which is gone as well. Will test the packages asap. Sebastian
Re: GinkgoCADx is finished :(
Hello Dmitry, Subject: GinkgoCADx is finished :( That is _really_ a pity. In case that's really it for GinkgoCADx let me thank you here and now for the work you have put into this package until this day. Karsten Today I've learned that MetaEmotion (developer of Ginkgo CADx) was acquired by Nielsen [1] who apparently have no interest in medical software (Ginkgo CADx in particular) and seems to have no appreciation to free software. Development of Ginkgo CADx appears to be ceased and most likely there will be no new releases. If anyone wants to fork GinkgoCADx, now will be a good time to do so. -- ## Current status in Debian: I've updated ginkgocadx repository with fixes required to build it with libinsighttoolkit4-dev and with GCC-5. Due to current state of GCC-5 transition it is not yet possible to build ginkgocadx in sid because of unmet dependencies: libstdc++6 : Breaks: libinsighttoolkit4.7 (= 4.7.2-2) but 4.7.2-2 is to be installed. The biggest problem is that something else has changed and -DNDEBUG no longer helps to avoid asserts with WX-3.0 so GinkgoCADx crashes with errors like this: usr/include/wx-3.0/wx/strvararg.h(456): assert (argtype (wxFormatStringSpecifierT::value)) == argtype failed in wxArgNormalizer(): format specifier doesn't match argument type Unfortunately I can't fix those type mismatches on my own... [1]: http://www.bloomberg.com/research/stocks/private/snapshot.asp?privcapId=303052091 -- Regards, Dmitry Smirnov. --- The truth is incontrovertible, malice may attack it, ignorance may deride it, but in the end; there it is. -- Winston Churchill -- GPG key ID E4071346 @ eu.pool.sks-keyservers.net E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150805193726.ga2...@hermes.hilbert.loc
GinkgoCADx is finished :(
Hi team, Today I've learned that MetaEmotion (developer of Ginkgo CADx) was acquired by Nielsen [1] who apparently have no interest in medical software (Ginkgo CADx in particular) and seems to have no appreciation to free software. Development of Ginkgo CADx appears to be ceased and most likely there will be no new releases. If anyone wants to fork GinkgoCADx, now will be a good time to do so. -- ## Current status in Debian: I've updated ginkgocadx repository with fixes required to build it with libinsighttoolkit4-dev and with GCC-5. Due to current state of GCC-5 transition it is not yet possible to build ginkgocadx in sid because of unmet dependencies: libstdc++6 : Breaks: libinsighttoolkit4.7 (= 4.7.2-2) but 4.7.2-2 is to be installed. The biggest problem is that something else has changed and -DNDEBUG no longer helps to avoid asserts with WX-3.0 so GinkgoCADx crashes with errors like this: usr/include/wx-3.0/wx/strvararg.h(456): assert (argtype (wxFormatStringSpecifierT::value)) == argtype failed in wxArgNormalizer(): format specifier doesn't match argument type Unfortunately I can't fix those type mismatches on my own... [1]: http://www.bloomberg.com/research/stocks/private/snapshot.asp?privcapId=303052091 -- Regards, Dmitry Smirnov. --- The truth is incontrovertible, malice may attack it, ignorance may deride it, but in the end; there it is. -- Winston Churchill signature.asc Description: This is a digitally signed message part.
Please help to nail GinkgoCADx bugs in Debian
Hi Carlos, It's been a while but we need your help again to squash some bugs in GinkgoCADx. I'm especially concerned about recent FTBFS in unstable: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=789932 as well as about FTBFS with GCC-5: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777876 Also there is an old (unfixed for a while) problem with displaying studies: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=753809 You can find list of all GinkgoCADx bugs here: https://bugs.debian.org/cgi-bin/pkgreport.cgi?src=ginkgocadx I hope you'll be able to help. Thank you. -- Regards, Dmitry Smirnov --- If any remedy is tested under controlled scientific conditions and proved to be effective, it will cease to be alternative and will simply become medicine. So-called alternative medicine either hasn't been tested or it has failed its tests. -- Richard Dawkins, 2007 signature.asc Description: This is a digitally signed message part.
Re: Source code of GinkgoCADx 3.7?
Hi, Andreas. Yes, there are. The problem is that we use GTK2 backend, and default is GTK3. It should be transparent but there is a component which needs directly access to the backend to perform some tasks (GL Context issues, window decoupling... etc.). BTW: We will upload the source soon as posible. Best regards. On Sun, Jun 29, 2014 at 12:15 PM, Andreas Tille andr...@an3as.eu wrote: Hi Carlos, I would like to inform you that the Debian package for GinkgoCADx 3.6.1 is now linked against wx3.0 which might have some side effects which only might become visible when using it intensively. So if you have users of the Debian package please ask them to be quite carefully in reporting any problems. I also noticed that a new upstream version is out but SF is not yet mirroring the source. Kind regards Andreas. -- http://fam-tille.de -- *Carlos Barrales Ruiz*carlos.barra...@metaemotion.com [+34] 983 108 494 *MetaEmotion*Edificio CTTA. Módulos 119-122. Paseo de Belén, nº9. E47011. Valladolid. Spain. www.metaemotion.com
Source code of GinkgoCADx 3.7?
Hi Carlos, I would like to inform you that the Debian package for GinkgoCADx 3.6.1 is now linked against wx3.0 which might have some side effects which only might become visible when using it intensively. So if you have users of the Debian package please ask them to be quite carefully in reporting any problems. I also noticed that a new upstream version is out but SF is not yet mirroring the source. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140629101502.ge6...@an3as.eu
ginkgocadx not in testing
Hi all, Just a quick question. I observed that ginkgocadx ist not yet in testing. While no big problem I wonder how this fits together. ginkgocadx is wating for gdcm. however for gdcm at http://packages.qa.debian.org/g/gdcm.html it reads This package is neither part of unstable nor experimental. This probably means that the package has been removed (or has been renamed). Thus the information here is of little interest ... the package is going to disappear unless someone takes it over and reintroduces it into unstable. testing migration excuses: Too young, only 0 of 10 days old Not considered Depends: gdcm libav (not considered) Depends: gdcm libav-extra (not considered) Is this a problem ? Best regards, Sebastian
Re: ginkgocadx not in testing
Sebastian, I am not sure this will fix everything, but I am planning on another upload on GDCM in the next hours. Hopefully GDCM will finally compile on plaforms without mono. Thanks for your patience. On Wed, Sep 7, 2011 at 7:58 PM, Sebastian Hilbert sebastian.hilb...@gmx.net wrote: Hi all, Just a quick question. I observed that ginkgocadx ist not yet in testing. While no big problem I wonder how this fits together. ginkgocadx is wating for gdcm. however for gdcm at http://packages.qa.debian.org/g/gdcm.html it reads This package is neither part of unstable nor experimental. This probably means that the package has been removed (or has been renamed). Thus the information here is of little interest ... the package is going to disappear unless someone takes it over and reintroduces it into unstable. testing migration excuses: Too young, only 0 of 10 days old Not considered Depends: gdcm libav (not considered) Depends: gdcm libav-extra (not considered) Is this a problem ? Best regards, Sebastian -- Mathieu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/ca+7wuswwny226v9d1ulym1hom9d77q04ewk0btr5pj7saq9...@mail.gmail.com
Re: Ginkgo-CADx - we are not there (Was: CMake library dependency files; ginkgocadx experimental build, testers wanted!)
Hi Michael, On Mon, Aug 08, 2011 at 10:33:36PM +0200, Michael Schutte wrote: build-deps don’t fail any more, the more elegant (AFAICT) approach involves upgrading to an apparently better way to use CMake. I am currently trying this for VTK by cherry-picking commits from the upstream VCS. It seems to work out more or less, but it interferes with ... This approach sounds quite promising and - provided the current VTK maintainers are supporting your work - will most probably lead to a reasonable solution from what I have read about all those problems. Please keep on with this work if you have time. Many thanks Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110809062054.ga31...@an3as.eu
Re: Ginkgo-CADx - we are not there (Was: CMake library dependency files; ginkgocadx experimental build, testers wanted!)
On Sun, 7 Aug 2011, Andreas Tille wrote: I just tried another test but things did not changed regarding the Socket.cpp.o -c /tmp/buildd/ginkgocadx-2.5.2.0/src/cadxcore/xmlrpc/XmlRpcSocket.cpp make[3]: *** No rule to make target `/usr/lib/libpng.so', needed by `src/cadxcore/libCADxCore.so.2.5.2.0'. Stop. problem. I tried to change USE_CUSTOM_* in CMakeLists.txt, but just got compile errors ... Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/pine.lnx.4.64.1108082150280.11...@tor.gallien.in-chemnitz.de
Re: Ginkgo-CADx - we are not there (Was: CMake library dependency files; ginkgocadx experimental build, testers wanted!)
On Sonntag, 7. August 2011 00:35:43 Andreas Tille wrote: Hi, did anybody tested the packages prepared by Michael in real life? I just tried another test but things did not changed regarding the Socket.cpp.o -c /tmp/buildd/ginkgocadx-2.5.2.0/src/cadxcore/xmlrpc/XmlRpcSocket.cpp make[3]: *** No rule to make target `/usr/lib/libpng.so', needed by `src/cadxcore/libCADxCore.so.2.5.2.0'. Stop. problem. So we need to keep on working / testing on this. Kind regards Andreas. On Mon, Jul 25, 2011 at 07:26:41PM +0200, Michael Schutte wrote: Hi Karsten, On Mon, Jul 25, 2011 at 06:37:45PM +0200, Karsten Hilbert wrote: In a first attempt to figure out #635300, I tried to build ginkgocadx without the presence of *LibraryDepends.cmake files in ITK and VTK. Turns out it seems to work, but without suitable example data http://www.aycan.de/main/lp/sample_dicom_images.html http://pubimage.hcuge.ch:8080/ I actually tested it with some example files a bit after posting my mail, but thanks nonetheless. Still, an “everything works as before” from an actual user (or otherwise knowledgable person) of the program would be nice to hear before changing three packages. Cheers, I have tested the packages that are available for amd64. Worked ok in real life. Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201108071143.25305.sebastian.hilb...@gmx.net
Ginkgo-CADx - we are not there (Was: CMake library dependency files; ginkgocadx experimental build, testers wanted!)
Hi,
did anybody tested the packages prepared by Michael in real life?
I just tried another test but things did not changed regarding the
Socket.cpp.o -c
/tmp/buildd/ginkgocadx-2.5.2.0/src/cadxcore/xmlrpc/XmlRpcSocket.cpp
make[3]: *** No rule to make target `/usr/lib/libpng.so', needed by
`src/cadxcore/libCADxCore.so.2.5.2.0'. Stop.
problem. So we need to keep on working / testing on this.
Kind regards
Andreas.
On Mon, Jul 25, 2011 at 07:26:41PM +0200, Michael Schutte wrote:
Hi Karsten,
On Mon, Jul 25, 2011 at 06:37:45PM +0200, Karsten Hilbert wrote:
In a first attempt to figure out #635300, I tried to build ginkgocadx
without the presence of *LibraryDepends.cmake files in ITK and VTK.
Turns out it seems to work, but without suitable example data
http://www.aycan.de/main/lp/sample_dicom_images.html
http://pubimage.hcuge.ch:8080/
I actually tested it with some example files a bit after posting my
mail, but thanks nonetheless. Still, an “everything works as before”
from an actual user (or otherwise knowledgable person) of the program
would be nice to hear before changing three packages.
Cheers,
--
Michael Schutte | michi@{uiae.at,debian.org}
Innsbruck, Austria| happily accepting encrypted mail
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Re: Please do Screenshots (GinkgoCADx, GNUmed?, BioInformatics program)
On Mon, Aug 01, 2011 at 12:03:01AM +0200, Steffen Möller wrote: 1. GNUmed: There are some at screenshots.debian.net - please make sure they are up to date and show GNUmed as it should be represented. 2. GinkgoCADx: YOu can not (yet) upload it to screenshots.debian.net because it seems to be a manual inclusion process and it has not yet done. However, you can prepare such an upload by doing the screenshot now and send it to me. Maybe Karsten and Sebastian can help? Sebastian did in private mail. 3. The journalist finally raised his eyebrows and said: This is really interesting. when I told him that the biological software finally can be used to detect EHEC strains and said This is really important. Please if anybody can do this, can you prepare a screenshot of a program dealing with investigation in EHEC? This may be a missunderstanding from my blog entries. Open Source bioinformatics can do all that. But we are not there, yet. I'd love to be there, though, which is what I am aiming at for 2012: complete medically relevant workflows that can be run by a non-bioinformatics IT student at the medical professional's side. So if it is not about a full workflow - can we have at least one part of the work in some a screenshot which just gives an idea of a program dealing with sequenzes. This means a wiki page with screenshots to follow and/or Taverna+Galaxy implementing such protocols. This is also why I am so much after Jalview getting in - it blocks Taverna :) So if you are after Jalview, could you please give a short summary about the current status? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110802063726.ga2...@an3as.eu
Re: Please do Screenshots (GinkgoCADx, GNUmed?, BioInformatics program)
Hi Andreas, On 07/31/2011 06:57 AM, Andreas Tille wrote: before I'll blog a report about the Debian Med BOF @ DebConf (probably not before Tuesday when I'm back home) I would like to call for your help. I had lunch with a journalist which was hopefully interesting enough for him. He finally asked me for screenshots of some relevant packages. If you ask me we should care for the following: 1. GNUmed: There are some at screenshots.debian.net - please make sure they are up to date and show GNUmed as it should be represented. 2. GinkgoCADx: YOu can not (yet) upload it to screenshots.debian.net because it seems to be a manual inclusion process and it has not yet done. However, you can prepare such an upload by doing the screenshot now and send it to me. Maybe Karsten and Sebastian can help? 3. The journalist finally raised his eyebrows and said: This is really interesting. when I told him that the biological software finally can be used to detect EHEC strains and said This is really important. Please if anybody can do this, can you prepare a screenshot of a program dealing with investigation in EHEC? This may be a missunderstanding from my blog entries. Open Source bioinformatics can do all that. But we are not there, yet. I'd love to be there, though, which is what I am aiming at for 2012: complete medically relevant workflows that can be run by a non-bioinformatics IT student at the medical professional's side. This means a wiki page with screenshots to follow and/or Taverna+Galaxy implementing such protocols. This is also why I am so much after Jalview getting in - it blocks Taverna :) EHEC could/should indeed be a start. It was the start for my thinking about it :) More interesting than EHEC (the last patient was release a day or two ago) is the bug coming next. For such emergencies there should be an infrastructure readily available for everyone to compare the local wet-lab expertise with what is special in our creepy animal. I cannot prove it, but it seems plausible to me that there is no automatism for a cure. And Open Source technologies widely available to inspect the previously unseen, i.e. a direct interface to Crowd Intelligence, may be something we just want since there is no time to waste. Best, Steffen -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4e35d115.8020...@gmx.de
Please do Screenshots (GinkgoCADx, GNUmed?, BioInformatics program)
Hi, before I'll blog a report about the Debian Med BOF @ DebConf (probably not before Tuesday when I'm back home) I would like to call for your help. I had lunch with a journalist which was hopefully interesinting enough for him. He finally asked me for screenshots of some relevant packages. If you ask me we should care for the following: 1. GNUmed: There are some at screenshots.debian.net - please make sure they are up to date and show GNUmed as it should be represented. 2. GinkgoCADx: YOu can not (yet) upload it to screenshots.debian.net because it seems to be a manual inclusion process and it has not yet done. However, you can prepare such an upload by doing the screenshot now and send it to me. 3. The journalist finally raised his eyebrows and said: This is really interesting. when I told him that the biological software finally can be used to detect EHEC strains and said This is really important. Please if anybody can do this, can you prepare a screenshot of a program dealing with investigation in EHEC? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110731045734.ga22...@an3as.eu
CMake library dependency files; ginkgocadx experimental build, testers wanted!
Hi everyone!
In a first attempt to figure out #635300, I tried to build ginkgocadx
without the presence of *LibraryDepends.cmake files in ITK and VTK.
Turns out it seems to work, but without suitable example data, I’m
unable to say for sure. I’d be grateful if some of you with experience
in the field could download, install and test
http://people.debian.org/~michi/ginkgocadx_2.5.1.0-1+nolibdeps1_amd64.deb
Before unpacking, you can verify the integrity of your download by also
getting
http://people.debian.org/~michi/ginkgocadx_2.5.1.0-1+nolibdeps1_amd64.deb.asc
and running
gpgv --keyring /usr/share/keyrings/debian-keyring.gpg
ginkgocadx_2.5.1.0-1+nolibdeps1_amd64.deb.asc
As for an actual solution, I guess that insighttoolkit, vtk and paraview
(probably others, I haven’t done a thorough search) should be fixed as
suggested in #506992. I would be happy about every input on this.
Cheers,
--
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Re: CMake library dependency files; ginkgocadx experimental build, testers wanted!
In a first attempt to figure out #635300, I tried to build ginkgocadx without the presence of *LibraryDepends.cmake files in ITK and VTK. Turns out it seems to work, but without suitable example data http://www.aycan.de/main/lp/sample_dicom_images.html http://pubimage.hcuge.ch:8080/ Does that help ? Karsten -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110725163745.36...@gmx.net
Re: CMake library dependency files; ginkgocadx experimental build, testers wanted!
Hi Karsten,
On Mon, Jul 25, 2011 at 06:37:45PM +0200, Karsten Hilbert wrote:
In a first attempt to figure out #635300, I tried to build ginkgocadx
without the presence of *LibraryDepends.cmake files in ITK and VTK.
Turns out it seems to work, but without suitable example data
http://www.aycan.de/main/lp/sample_dicom_images.html
http://pubimage.hcuge.ch:8080/
I actually tested it with some example files a bit after posting my
mail, but thanks nonetheless. Still, an “everything works as before”
from an actual user (or otherwise knowledgable person) of the program
would be nice to hear before changing three packages.
Cheers,
--
Michael Schutte | michi@{uiae.at,debian.org}
Innsbruck, Austria| happily accepting encrypted mail
OpenPGP: 0x16fb 517b a866 c3f6 8f11 1485 f3e4 122f 1D8C 261A
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Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
Am Freitag, 15. Juli 2011, 09:46:58 schrieb Sebastian Hilbert: Am Donnerstag, 14. Juli 2011, 17:01:31 schrieb Andreas Tille: On Thu, Jul 14, 2011 at 03:52:41PM +0200, Carlos Barrales Ruiz wrote: Hi, All. We have just uploaded the ginkgocadx 2.5.1.0 release. Great. Now it also compiles in unstable again!!! = Just ploaded to unstable. The rpath patches have been applied with a few bug fixes and a small feature too (dicomization flow reprocessing). One remaining rpath issue is left in the patch set - please make sure you will take over in your next release. We were able to built the .deb for i386 arch with no errors (just the old friends dpkg-shlibdeps warnings). We use latest updated (today) debian unstable. I hope that autobuilders will care for i386 (and other arches). Hope it works for you all. Me too. Thanks for the notification Seems to work. Thanks to everyone involved to make this happen. There now seems to be a new upstream version 2.5.2. Did the watch file catch this ? Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201107240840.22153.sebastian.hilb...@gmx.net
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
On Sun, Jul 24, 2011 at 08:40:20AM +0200, Sebastian Hilbert wrote: There now seems to be a new upstream version 2.5.2. Did the watch file catch this ? It is (which you can perfectly test via `uscan --verbose`), but the tasks pages might have 1-2 days delay (in worst case) because a cron job at first needs to update UDD and than the tasks pages will be updated only once a day. Thus pinging the list if it is important to you might always help. Thanks for the notification and greetings from Banja Luka Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110724085620.gb27...@an3as.eu
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
On Sun, 24 Jul 2011, Andreas Tille wrote: Thus pinging the list if it is important to you might always help. It does not build here. /usr/lib/libpng.so is needed but only /usr/lib/i386-linux-gnu/libpng.so is available. The multiarch support was added on 19.07. in libpng ... Thorsten -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/pine.lnx.4.64.1107241902380.8...@tor.gallien.in-chemnitz.de
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
On Sun, Jul 24, 2011 at 07:06:22PM +0200, Thorsten Alteholz wrote: It does not build here. /usr/lib/libpng.so is needed but only /usr/lib/i386-linux-gnu/libpng.so is available. The multiarch support was added on 19.07. in libpng ... Same here. It builds fine on my testing system but fails with the same error as reported above. Besides that I continue to fail seeing a reason in this multiarch business and do not know how to circumvent such hassle it might be reasonable to wait until ginkgocadx propagated in the current version to testing anyway. Once this happened we might try again (any immediate solution is welcome anyway). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110724192231.gi27...@an3as.eu
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
On Sun, Jul 24, 2011 at 3:22 PM, Andreas Tille andr...@an3as.eu wrote: On Sun, Jul 24, 2011 at 07:06:22PM +0200, Thorsten Alteholz wrote: It does not build here. /usr/lib/libpng.so is needed but only /usr/lib/i386-linux-gnu/libpng.so is available. The multiarch support was added on 19.07. in libpng ... Same here. It builds fine on my testing system but fails with the same error as reported above. Besides that I continue to fail seeing a reason in this multiarch business and do not know how to circumvent such hassle it might be reasonable to wait until ginkgocadx propagated in the current version to testing anyway. Once this happened we might try again (any immediate solution is welcome anyway). Hi Andreas, This can be solved by rebuilding (or better fixing) vtk and/or insighttoolkit. Both libraries are exporting their dependencies and force your package to build against the same path. If the library gets moved around e.g. from /usr/lib/libpng.so to /usr/lib/i386-linux-gnu/libpng.so you will get a build error. If you want to fix it you have to touch their internal cmake code. The problem exists since a long time and the multiarch project makes it more visible. You can read more about it here: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=629815 Cheers Dominique -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caavalczca7wwyy-z7zajzgelwyip1swnr93fizu5bzu8jj4...@mail.gmail.com
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
On Sun, Jul 24, 2011 at 03:49:32PM -0400, Dominique Belhachemi wrote: This can be solved by rebuilding (or better fixing) vtk and/or insighttoolkit. Both libraries are exporting their dependencies and force your package to build against the same path. If the library gets moved around e.g. from /usr/lib/libpng.so to /usr/lib/i386-linux-gnu/libpng.so you will get a build error. If you want to fix it you have to touch their internal cmake code. Thanks for the hint. While insighttoolkit is under our control could somebody try this? The problem exists since a long time and the multiarch project makes it more visible. You can read more about it here: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=629815 I considered this bug fixed because we finally got ginkgocadx compiled. I did not expected that it will come up over and over with png (and jpg and tiff and whatever libraries we depend from). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110724203557.gk27...@an3as.eu
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
Hi,
On Sun, Jul 24, 2011 at 10:35:57PM +0200, Andreas Tille wrote:
On Sun, Jul 24, 2011 at 03:49:32PM -0400, Dominique Belhachemi wrote:
This can be solved by rebuilding (or better fixing) vtk and/or
insighttoolkit.
Both libraries are exporting their dependencies and force your package
to build against the same path. If the library gets moved around e.g.
from /usr/lib/libpng.so to /usr/lib/i386-linux-gnu/libpng.so you will
get a build error. If you want to fix it you have to touch their
internal cmake code.
Thanks for the hint. While insighttoolkit is under our control could
somebody try this?
I’ll open a bug to keep this on the radar. At the first glance, the
build system seems awfully complicated, but perhaps one can grep their
way through it …
Cheers,
--
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Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
Hi, On Sun, Jul 24, 2011 at 10:56:52PM +0200, Michael Schutte wrote: I’ll open a bug to keep this on the radar. At the first glance, the build system seems awfully complicated, but perhaps one can grep their way through it … I'd proxy the promised Pizza + Beer offer to you if you would manage this here at DebConf. Wait - I guess you will probably not want an additional meal while I'm wondering which one I should skip. Just feel free to bother me about another drink. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110724210206.gl27...@an3as.eu
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
Andreas,
On Sun, Jul 24, 2011 at 11:02:06PM +0200, Andreas Tille wrote:
I'd proxy the promised Pizza + Beer offer to you if you would manage
this here at DebConf. Wait - I guess you will probably not want an
additional meal while I'm wondering which one I should skip. Just
feel free to bother me about another drink.
Well, thanks; I wasn’t aware of this offer until now, but I’m already
stuffed each and every day!
I’ll definitely have a look, but you might easily save the KM for a
drink as well, given that this whole CMake stuff might just be way over
my head :-)
Cheers,
--
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Innsbruck, Austria| happily accepting encrypted mail
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Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
On Sun, Jul 24, 2011 at 11:02:06PM +0200, Andreas Tille wrote: I’ll open a bug to keep this on the radar. At the first glance, the build system seems awfully complicated, but perhaps one can grep their way through it … I'd proxy the promised Pizza + Beer offer to you if you would manage this here at DebConf. Yes, please ! Karsten -- GPG key ID E4071346 @ gpg-keyserver.de E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110724211235.gg2...@hermes.hilbert.loc
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
Am Donnerstag, 14. Juli 2011, 17:01:31 schrieb Andreas Tille: On Thu, Jul 14, 2011 at 03:52:41PM +0200, Carlos Barrales Ruiz wrote: Hi, All. We have just uploaded the ginkgocadx 2.5.1.0 release. Great. Now it also compiles in unstable again!!! = Just ploaded to unstable. The rpath patches have been applied with a few bug fixes and a small feature too (dicomization flow reprocessing). One remaining rpath issue is left in the patch set - please make sure you will take over in your next release. We were able to built the .deb for i386 arch with no errors (just the old friends dpkg-shlibdeps warnings). We use latest updated (today) debian unstable. I hope that autobuilders will care for i386 (and other arches). Hope it works for you all. Me too. Thanks for the notification Seems to work. Thanks to everyone involved to make this happen. Best regards, Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201107150946.59053.sebastian.hilb...@gmx.net
ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
Hi, All. We have just uploaded the ginkgocadx 2.5.1.0 release. The rpath patches have been applied with a few bug fixes and a small feature too (dicomization flow reprocessing). We were able to built the .deb for i386 arch with no errors (just the old friends dpkg-shlibdeps warnings). We use latest updated (today) debian unstable. Hope it works for you all. El 12/07/2011, a las 16:48, Andreas Tille wrote: I tried to work around so called lintian errors (lintian is the Debian tool which checks for things you should not do) about useless RPATH definitions. I was partly successfull and I would like you to incorporate the patches I copied to http://people.debian.org/~tille/packages/ginkgocadx/debian/patches/ into your next point release. These patches are leaving the following lintian-critical errors: E: ginkgocadx: binary-or-shlib-defines-rpath usr/bin/ginkgocadx /usr/lib/InsightToolkit E: ginkgocadx: binary-or-shlib-defines-rpath usr/bin/ginkgocadx /usr/lib/vtk-5.6 So if some cmake expert has an idea how to drop even these explicte links I'd be happy. Currently I'm hacking around this issue via /usr/bin/chrpath -r /usr/lib/ginkgocadx debian/ginkgocadx/usr/bin/ginkgocadx which is really not the most elegant way to do this. -- Carlos Barrales Ruiz. carlos.barra...@metaemotion.com http://healthcare.metaemotion.com/ -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/1c4f5510-bd8d-4cc9-a052-056409b67...@metaemotion.com
Re: ginkgocadx-2.5.1.0.tgz released. was: (ginkgocadx-2.5.0.1.tgz released)
On Thu, Jul 14, 2011 at 03:52:41PM +0200, Carlos Barrales Ruiz wrote: Hi, All. We have just uploaded the ginkgocadx 2.5.1.0 release. Great. Now it also compiles in unstable again!!! = Just ploaded to unstable. The rpath patches have been applied with a few bug fixes and a small feature too (dicomization flow reprocessing). One remaining rpath issue is left in the patch set - please make sure you will take over in your next release. We were able to built the .deb for i386 arch with no errors (just the old friends dpkg-shlibdeps warnings). We use latest updated (today) debian unstable. I hope that autobuilders will care for i386 (and other arches). Hope it works for you all. Me too. Thanks for the notification Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110714150131.ge1...@an3as.eu
Re: ginkgocadx-2.5.0.1.tgz released
Hi Andreas,
Taking this to the list.
Am Dienstag, 12. Juli 2011, 13:47:42 schrieb Andreas Tille:
On Tue, Jul 12, 2011 at 12:02:38PM +0200, Carlos Barrales wrote:
Thank you. will follow your steps.
Feel free to ask questions like this at debian-med list. We are
keen on helping you here.
Sorry about that. Another thing I missed. Whould you mind to try fixing
it?
-8--
-- ---
lightvisualizator/CMakeLists.txt(revisión: 3973)
+++ lightvisualizator/CMakeLists.txt(copia de trabajo)
@@ -31,11 +31,11 @@
IF(LINUX AND NOT CUSTOM_PACKAGE)
SET(CMAKE_SKIP_BUILD_RPATH FALSE)
SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-SET(CMAKE_INSTALL_RPATH
${CMAKE_INSTALL_PREFIX}/share/ginkgocadx/bin) +
SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib/ginkgocadx)
SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES
${CMAKE_INSTALL_PREFIX}/share/ginkgocadx/bin isSystemDir)
+LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES
${CMAKE_INSTALL_PREFIX}/lib/ginkgocadx isSystemDir)
IF(${isSystemDir} STREQUAL -1)
-SET(CMAKE_INSTALL_RPATH
${CMAKE_INSTALL_PREFIX}/share/ginkgocadx/bin)
+SET(CMAKE_INSTALL_RPATH
${CMAKE_INSTALL_PREFIX}/lib/ginkgocadx)
ENDIF()
ENDIF()
-8--
--
This now works and package compiles.
@ Andreas
Are you saying it compiles on your system again ? Would you mind uploading it
somewhere so I can get it and try to compile it ?
Sebastian
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Re: ginkgocadx-2.5.0.1.tgz released
On Tue, Jul 12, 2011 at 02:36:01PM +0200, Hilbert, Sebastian wrote: Taking this to the list. ... @ Andreas Are you saying it compiles on your system again ? That's quite possible. There's been a lot of re-compiling for multi-arch and NMUing going on at Debian lately, one of which was vtk. Karsten -- GPG key ID E4071346 @ gpg-keyserver.de E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110712124937.gc2...@hermes.hilbert.loc
Re: ginkgocadx-2.5.0.1.tgz released
On Tue, Jul 12, 2011 at 02:36:01PM +0200, Sebastian Hilbert wrote: Are you saying it compiles on your system again ? I'm able to build the package on my (specific) system which is not affected by the libvtk5-dev issue (#629815) but I'm working down a list of lintian errors about wrong RPATH definitions (I just catched 10 out of 12). This might helpd upstream to issue a rpath clean release and will spare us extra patches. Would you mind uploading it somewhere so I can get it and try to compile it ? Sure I'll do (either after having all RPATH definitions removed or in the current state - which is reflected in SVN). However most people will fail building the package because of #629815. There is some hope in the end of the bug log - but making some more noise there might not harm. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110712135451.ga11...@an3as.eu
Re: ginkgocadx-2.5.0.1.tgz released
On Tue, Jul 12, 2011 at 02:49:37PM +0200, Karsten Hilbert wrote: That's quite possible. There's been a lot of re-compiling for multi-arch and NMUing going on at Debian lately, one of which was vtk. To say it clearly: The package does not build in my unstable pbuilder environment and not on recently updated testing machines. The only thing which works for me is a *not* recently updated testing machine. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110712135655.gb11...@an3as.eu
Re: ginkgocadx-2.5.0.1.tgz released
Hi Carlos, On Tue, Jul 12, 2011 at 12:02:38PM +0200, Carlos Barrales wrote: We think is best we release (.2) a new one fixing all this issues. I tried to work around so called lintian errors (lintian is the Debian tool which checks for things you should not do) about useless RPATH definitions. I was partly successfull and I would like you to incorporate the patches I copied to http://people.debian.org/~tille/packages/ginkgocadx/debian/patches/ into your next point release. These patches are leaving the following lintian-critical errors: E: ginkgocadx: binary-or-shlib-defines-rpath usr/bin/ginkgocadx /usr/lib/InsightToolkit E: ginkgocadx: binary-or-shlib-defines-rpath usr/bin/ginkgocadx /usr/lib/vtk-5.6 So if some cmake expert has an idea how to drop even these explicte links I'd be happy. Currently I'm hacking around this issue via /usr/bin/chrpath -r /usr/lib/ginkgocadx debian/ginkgocadx/usr/bin/ginkgocadx which is really not the most elegant way to do this. For those who want to test the package on amd64 they could give the package at http://people.debian.org/~tille/packages/ginkgocadx a try. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110712144823.gc11...@an3as.eu
Re: Medical imaging experts please check mimetype for GinkgoCADx (r7121)
Hi Karsten, On Wed, Jun 22, 2011 at 10:24:12PM +0200, Karsten Hilbert wrote: grep -i dicom /usr/share/mime-info/* /usr/share/mime-info/gnome-vfs.keys: [it]description=Immagine DICOM /usr/share/mime-info/gnome-vfs.keys: [sq]description=Figurë Digital Imaging and Communications in Medicine (DICOM) /usr/share/mime-info/gnome-vfs.keys: [tr]description=DICOM resim /usr/share/mime-info/gnome-vfs.keys: [zh_TW]description=DICOM 醫學影像 grep -i dicom /usr/share/mime/* /usr/share/mime/generic-icons:application/dicom:image-x-generic /usr/share/mime/globs:application/dicom:*.dcm /usr/share/mime/globs2:50:application/dicom:*.dcm Übereinstimmungen in Binärdatei /usr/share/mime/magic. Übereinstimmungen in Binärdatei /usr/share/mime/mime.cache. /usr/share/mime/types:application/dicom But what exactly does this mean for the two files I commited??? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110623060054.gb32...@an3as.eu
Re: Medical imaging experts please check mimetype for GinkgoCADx (r7121)
On Thu, Jun 23, 2011 at 08:00:54AM +0200, Andreas Tille wrote: But what exactly does this mean for the two files I commited??? AFAICT Debian already knows the DICOM mime type so there's no need to add magic: grep -i dicom /usr/share/mime/* Übereinstimmungen in Binärdatei /usr/share/mime/magic. Karsten -- GPG key ID E4071346 @ gpg-keyserver.de E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110623062320.ga2...@hermes.hilbert.loc
compiling ginkgocadx
Hi all, I tried to locally build ginkgocadx via dget -xu foo/ginkgocadx-foo.dsc This led to downloading and unpacking of sources. in subdir src I added I set CMAKE_BUILD_TYPE to debug Then I tried. debuild -b in the debian directory which led to ... iles/CADxCore.dir/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp.o -c /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp In file included from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gdk/gdkprivate.h:30, from /usr/include/gtk-2.0/gdk/gdkx.h:30, from /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp:141: /usr/include/gtk-2.0/gdk/gdkpixbuf.h:37:35: error: gdk-pixbuf/gdk-pixbuf.h: Datei oder Verzeichnis nicht gefunden In file included from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gdk/gdkprivate.h:30, from /usr/include/gtk-2.0/gdk/gdkx.h:30, from /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp:141: /usr/include/gtk-2.0/gdk/gdkpixbuf.h:73: error: ‘GdkPixbufAlphaMode’ has not been declared make[3]: *** [src/cadxcore/CMakeFiles/CADxCore.dir/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp.o] Fehler 1 make[3]: Leaving directory `/home/tux/Sources/ginkgocadx-2.4.1.1/obj-x86_64- linux-gnu' make[2]: *** [src/cadxcore/CMakeFiles/CADxCore.dir/all] Fehler 2 make[2]: Leaving directory `/home/tux/Sources/ginkgocadx-2.4.1.1/obj-x86_64- linux-gnu' make[1]: *** [all] Fehler 2 make[1]: Leaving directory `/home/tux/Sources/ginkgocadx-2.4.1.1/obj-x86_64- linux-gnu' dh_auto_build: make -j1 returned exit code 2 make: *** [build] Fehler 2 dpkg-buildpackage: Fehler: Fehler-Exitstatus von debian/rules build war 2 debuild: fatal error at line 1325: dpkg-buildpackage -rfakeroot -D -us -uc -b failed Any help is appreciated. Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201106230835.28535.sebastian.hilb...@gmx.net
Re: compiling ginkgocadx
On Thu, Jun 23, 2011 at 08:35:28AM +0200, Sebastian Hilbert wrote: ... iles/CADxCore.dir/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp.o -c /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp In file included from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gdk/gdkprivate.h:30, from /usr/include/gtk-2.0/gdk/gdkx.h:30, from /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp:141: /usr/include/gtk-2.0/gdk/gdkpixbuf.h:37:35: error: gdk-pixbuf/gdk-pixbuf.h: Datei oder Verzeichnis nicht gefunden That's strange. The missing file is in $ apt-file search gdk-pixbuf/gdk-pixbuf.h libgdk-pixbuf2.0-dev: /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf.h but I'm quite sure this should have been pulled via dependencies. Are you sure that this package is installed? Kind regards Andreas. PS: It is a good idea to set LC_ALL=C when posting to lists with people who do not understand your language. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110623070553.ga2...@an3as.eu
Re: Medical imaging experts please check mimetype for GinkgoCADx (r7121)
Hi all, On Thu, Jun 23, 2011 at 8:23 AM, Karsten Hilbert karsten.hilb...@gmx.net wrote: On Thu, Jun 23, 2011 at 08:00:54AM +0200, Andreas Tille wrote: But what exactly does this mean for the two files I commited??? AFAICT Debian already knows the DICOM mime type so there's no need to add magic: DICOM does not define file extension (.dcm), but only recommends .dcm when storing on disk (rfc3240). What I would also encode is that DICOMDIR is a special file compare to other DICOM file (it is an index pointing to other DICOM files). i am guessing this is also a special case for ginkgo-cadx. It looks like `file` is capable of recognizing dicom file anyway: $ file --mime-type /tmp/BLA /tmp/BLA: application/dicom 2cts -- Mathieu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/banlktinhjuom-4rbzakq6io6ngarzri...@mail.gmail.com
Re: Medical imaging experts please check mimetype for GinkgoCADx (r7121)
On Thu, Jun 23, 2011 at 09:07:16AM +0200, Mathieu Malaterre wrote: DICOM does not define file extension (.dcm), but only recommends .dcm when storing on disk (rfc3240). That's the case with many file extensions, particularly on unix like systems. What I would also encode is that DICOMDIR is a special file compare to other DICOM file (it is an index pointing to other DICOM files). I wonder whether that is possible ? i am guessing this is also a special case for ginkgo-cadx. Yes. It looks like `file` is capable of recognizing dicom file anyway: $ file --mime-type /tmp/BLA /tmp/BLA: application/dicom Yes, that's what I was saying: Debian already knows the DICOM mime type. It recognizes files by looking for DICM within the first few bytes. Karsten -- GPG key ID E4071346 @ gpg-keyserver.de E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110623071641.gd2...@hermes.hilbert.loc
Re: compiling ginkgocadx
Am Donnerstag, 23. Juni 2011, 09:05:53 schrieb Andreas Tille: On Thu, Jun 23, 2011 at 08:35:28AM +0200, Sebastian Hilbert wrote: ... iles/CADxCore.dir/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp.o -c /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKR enderWindowInteractor.cpp In file included from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gdk/gdkprivate.h:30, from /usr/include/gtk-2.0/gdk/gdkx.h:30, from /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKR enderWindowInteractor.cpp:141: /usr/include/gtk-2.0/gdk/gdkpixbuf.h:37:35: error: gdk-pixbuf/gdk-pixbuf.h: Datei oder Verzeichnis nicht gefunden That's strange. The missing file is in $ apt-file search gdk-pixbuf/gdk-pixbuf.h libgdk-pixbuf2.0-dev: /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf.h but I'm quite sure this should have been pulled via dependencies. Are you sure that this package is installed? root@heartbeat:/home/tux/Sources/ginkgocadx-2.4.1.1/debian# apt-file search gdk-pixbuf/gdk-pixbuf.h l ibgdk-pixbuf2.0-dev: /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf.h libgfcui-dev: /usr/include/gfc-2.0/gfc/gdk-pixbuf/gdk-pixbuf.hh libgtk2.0-dev: /usr/include/gtk-2.0/gdk-pixbuf/gdk-pixbuf.h lsb-build-desktop3: /usr/include/lsb3/gtk-2.0/gdk-pixbuf/gdk-pixbuf.h root@heartbeat:/home/tux/Sources/ginkgocadx-2.4.1.1/debian# apt-cache policy libgdk-pixbuf2.0-dev libgdk-pixbuf2.0-dev: Installiert: 2.23.3-3 Kandidat:2.23.3-3 Versionstabelle: *** 2.23.3-3 0 650 http://ftp.de.debian.org/debian/ testing/main amd64 Packages 600 http://ftp.de.debian.org/debian/ unstable/main amd64 Packages 100 /var/lib/dpkg/status root@heartbeat:/home/tux/Sources/ginkgocadx-2.4.1.1/debian# apt-cache policy libgtk2.0-dev libgtk2.0-dev: Installiert: 2.24.4-3 Kandidat:2.24.4-3 Versionstabelle: *** 2.24.4-3 0 650 http://ftp.de.debian.org/debian/ testing/main amd64 Packages 600 http://ftp.de.debian.org/debian/ unstable/main amd64 Packages 100 /var/lib/dpkg/status 2.20.1-2 0 700 http://ftp.de.debian.org/debian/ squeeze/main amd64 Packages Beats me. Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201106230929.16922.sebastian.hilb...@gmx.net
Re: compiling ginkgocadx
On Thu, Jun 23, 2011 at 09:29:16AM +0200, Sebastian Hilbert wrote: That's strange. The missing file is in $ apt-file search gdk-pixbuf/gdk-pixbuf.h libgdk-pixbuf2.0-dev: /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf.h but I'm quite sure this should have been pulled via dependencies. Are you sure that this package is installed? After reading your error message again I think my answer did not really fit the problem anyway and so I tried to reproduce it. I was unable to reproduce it and thus compiled successfully. Please find a package containing unstripped binaries here: http://people.debian.org/~tille/packages/ginkgocadx/ Good luck Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110623073736.gb2...@an3as.eu
error: cannot read ginkgocadx-2.4.1.1/debian/patches/01_no_msse.patch: No such file or directory
Hi could someone please have a look at ginkgo-cadx package the patch series file reference 01_no_msse.patch which cannot be found... Thanks -- Mathieu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/BANLkTi=5coy_igf7u3phxbvpujcfjfx...@mail.gmail.com
Re: error: cannot read ginkgocadx-2.4.1.1/debian/patches/01_no_msse.patch: No such file or directory
On Thu, Jun 23, 2011 at 09:38:33AM +0200, Mathieu Malaterre wrote: Hi could someone please have a look at ginkgo-cadx package the patch series file reference 01_no_msse.patch which cannot be found... Done - sorry Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110623080600.gc2...@an3as.eu
Re: compiling ginkgocadx
opps... seems that CMake conditions IF(DEBUG) [...] are incompleted or wrong. Them should include any path Release does. Should easy to fix. The only thing to do is to check those control sentences and ensure nothing are missing. Would you mind to try it? Best regards. -- Carlos Barrales Ruiz. carlos.barra...@metaemotion.com Móvil: 654807575 http://healthcare.metaemotion.com On Thu, Jun 23, 2011 at 8:35 AM, Sebastian Hilbert sebastian.hilb...@gmx.net wrote: Hi all, I tried to locally build ginkgocadx via dget -xu foo/ginkgocadx-foo.dsc This led to downloading and unpacking of sources. in subdir src I added I set CMAKE_BUILD_TYPE to debug Then I tried. debuild -b in the debian directory which led to ... iles/CADxCore.dir/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp.o -c /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp In file included from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gdk/gdkprivate.h:30, from /usr/include/gtk-2.0/gdk/gdkx.h:30, from /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp:141: /usr/include/gtk-2.0/gdk/gdkpixbuf.h:37:35: error: gdk-pixbuf/gdk-pixbuf.h: Datei oder Verzeichnis nicht gefunden In file included from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gdk/gdkprivate.h:30, from /usr/include/gtk-2.0/gdk/gdkx.h:30, from /home/tux/Sources/ginkgocadx-2.4.1.1/src/cadxcore/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp:141: /usr/include/gtk-2.0/gdk/gdkpixbuf.h:73: error: ‘GdkPixbufAlphaMode’ has not been declared make[3]: *** [src/cadxcore/CMakeFiles/CADxCore.dir/VTKInria3D/wxVTK/wxVTKRenderWindowInteractor.cpp.o] Fehler 1 make[3]: Leaving directory `/home/tux/Sources/ginkgocadx-2.4.1.1/obj-x86_64- linux-gnu' make[2]: *** [src/cadxcore/CMakeFiles/CADxCore.dir/all] Fehler 2 make[2]: Leaving directory `/home/tux/Sources/ginkgocadx-2.4.1.1/obj-x86_64- linux-gnu' make[1]: *** [all] Fehler 2 make[1]: Leaving directory `/home/tux/Sources/ginkgocadx-2.4.1.1/obj-x86_64- linux-gnu' dh_auto_build: make -j1 returned exit code 2 make: *** [build] Fehler 2 dpkg-buildpackage: Fehler: Fehler-Exitstatus von debian/rules build war 2 debuild: fatal error at line 1325: dpkg-buildpackage -rfakeroot -D -us -uc -b failed Any help is appreciated. Sebastian
Re: compiling ginkgocadx
Am Donnerstag, 23. Juni 2011, 09:53:33 schrieb Carlos Barrales: opps... seems that CMake conditions IF(DEBUG) [...] are incompleted or wrong. Them should include any path Release does. Should easy to fix. The only thing to do is to check those control sentences and ensure nothing are missing. Would you mind to try it? I will check but since it did seem to work for Andreas ( I took it from his last mail that he has debug enable (?). it might be a problem with my system. If it is missing something on in debug mode it should work in release mode then ? BTW. The unstriped binaries Andreas provided did not get me a backtrace. I will provide more information in another mail. Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201106231011.38296.sebastian.hilb...@gmx.net
Re: compiling ginkgocadx
On Thu, Jun 23, 2011 at 10:11 AM, Sebastian Hilbert sebastian.hilb...@gmx.net wrote: I will check but since it did seem to work for Andreas ( I took it from his last mail that he has debug enable (?). Ok. it might be a problem with my system. If it is missing something on in debug mode it should work in release mode then ? Sure. BTW. The unstriped binaries Andreas provided did not get me a backtrace. I will provide more information in another mail. Ok, we stand for that. Thank you. Best regards. -- Carlos Barrales Ruiz. carlos.barra...@metaemotion.com Móvil: 654807575 http://healthcare.metaemotion.com
Re: compiling ginkgocadx
Am Donnerstag, 23. Juni 2011, 10:26:05 schrieb Andreas Tille: On Thu, Jun 23, 2011 at 10:11:37AM +0200, Sebastian Hilbert wrote: I will check but since it did seem to work for Andreas ( I took it from his last mail that he has debug enable (?). Perhaps I missinterpreted your hint to CMAKE_BUILD_TYPE when I added the following line to debian/rules: CMAKE_BUILD_TYPE = debug If you did something else it is clear why I did not run into the error ... But what probably really helped to keep the debug information was: override_dh_strip: echo Do not strip At least lintian is now awrning about not stripped executables. If I'm not missleaded there is a control variable which prevents dh_strip from doing its job but I never can remember its name and for a quick debugging shot this helps as well. BTW. The unstriped binaries Andreas provided did not get me a backtrace. Uhmmm, that smells like a quite ugly problem. Carlos, can you perhaps try the Debian package at http://packages.debian.org/sid/amd64/ginkgocadx/download (only for amd64). I will provide more information in another mail. Ahhh, hope you have some clue. After updating parts of my system to testing (e.g. for libvtk5-dev) it now errors out with the known cmake issue ( I think it pulled in a new cmake and libc6 along the line). Guess I will have to wait. I have sent valgrind logs to upstream (as suggested by upstream) so I hope a solution will come from their end. Thanks for the effort, Sebastian -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/201106231229.19491.sebastian.hilb...@gmx.net
Re: compiling ginkgocadx
On Thu, Jun 23, 2011 at 12:29:14PM +0200, Sebastian Hilbert wrote: After updating parts of my system to testing (e.g. for libvtk5-dev) it now errors out with the known cmake issue ( I think it pulled in a new cmake and libc6 along the line). Guess I will have to wait. Alternatively you can pull an older cmake version from http://snapshot.debian.org/binary/cmake/ I have sent valgrind logs to upstream (as suggested by upstream) so I hope a solution will come from their end. This would be optimal Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110623104706.gh2...@an3as.eu
Medical imaging experts please check mimetype for GinkgoCADx (r7121)
Hi,
I commited a fix for #631205. Can some DICOM expert please have a look
into this? Specifically I'm unsure about the description string.
I also wonder whether we yould provide some magic tag in
sharedmimeinfo - I just do not know this format.
Kind regards
Andreas.
- Forwarded message from Andreas Tille ti...@alioth.debian.org -
Date: Wed, 22 Jun 2011 17:31:05 +
To: debian-med-com...@lists.alioth.debian.org
From: Andreas Tille ti...@alioth.debian.org
X-Spam_score: -4.1
Subject: r7121 - trunk/packages/ginkgocadx/trunk/debian
Author: tille
Date: 2011-06-22 17:31:05 + (Wed, 22 Jun 2011)
New Revision: 7121
Added:
trunk/packages/ginkgocadx/trunk/debian/mime
trunk/packages/ginkgocadx/trunk/debian/sharedmimeinfo
Modified:
trunk/packages/ginkgocadx/trunk/debian/changelog
Log:
Added mime information - please verify correctness!
Modified: trunk/packages/ginkgocadx/trunk/debian/changelog
===
--- trunk/packages/ginkgocadx/trunk/debian/changelog2011-06-21 16:43:52 UTC
(rev 7120)
+++ trunk/packages/ginkgocadx/trunk/debian/changelog2011-06-22 17:31:05 UTC
(rev 7121)
@@ -1,3 +1,10 @@
+ginkgocadx (2.4.1.1-3) UNRELEASED; urgency=low
+
+ * debian/{mime,sharedmimeinfo}: Mime info for DICOM images
+Closes: #631205
+
+ -- Andreas Tille ti...@debian.org Wed, 22 Jun 2011 19:29:09 +0200
+
ginkgocadx (2.4.1.1-2) unstable; urgency=low
* debian/patches/01_no_msse.patch: Do not build with -msse flag
Added: trunk/packages/ginkgocadx/trunk/debian/mime
===
--- trunk/packages/ginkgocadx/trunk/debian/mime (rev 0)
+++ trunk/packages/ginkgocadx/trunk/debian/mime 2011-06-22 17:31:05 UTC (rev
7121)
@@ -0,0 +1 @@
+application/dicom; ginkgocadx '%s'; description=DICOM medical image;
nametemplate=%s.dcm
Added: trunk/packages/ginkgocadx/trunk/debian/sharedmimeinfo
===
--- trunk/packages/ginkgocadx/trunk/debian/sharedmimeinfo
(rev 0)
+++ trunk/packages/ginkgocadx/trunk/debian/sharedmimeinfo 2011-06-22
17:31:05 UTC (rev 7121)
@@ -0,0 +1,9 @@
+?xml version=1.0 encoding=UTF-8?
+mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'
+ mime-type type=application/dicom
+sub-class-of type=text/plain/
+commentDICOM medical image/comment
+comment xml:lang=deDICOM medizinisches Bild/comment
+glob pattern=*.dcm/
+ /mime-type
+/mime-info
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Bug#628106: ITP: ginkgocadx -- Medical Imaging Software and complete DICOM Viewer
Package: wnpp Severity: wishlist Owner: Andreas Tille ti...@debian.org * Package name: ginkgocadx Version : 2.4.1.1 Upstream Author : Carlos Barrales Ruiz carlos.barra...@metaemotion.com * URL : http://ginkgo-cadx.com/ * License : LGPL-2+ Programming Lang: C++ Description : Medical Imaging Software and complete DICOM Viewer Ginkgo CADx provides a complete DICOM Viewer solution with advanced capabilities and extensions support. . * Easy and customizable interface through profiles. * Full featured DICOM Image Visualization. * Complete tool set (measure, markers, text, ...). * Multiple modalities support (Neurological, Radiological, Dermathological, Ophthalmological, UltraSound, Endoscopy, ...) * Dicomization support from JPEG, PNG, GIF and TIFF. * Full EMH integration support: HL7 standard and IHE compliant workflows. * PACS Workstation (C-FIND, C-MOVE, C-STORE...) * Extensible throught custom Extensions. - Retinal image mosaic composition. - Automatic retinal analysis diagnostics. - Psoriasis automatic diagnostics. Remark: This package is maintained by the Debian Med team. The packaging is available in SVN svn://svn.debian.org/svn/debian-med/trunk/packages/ginkgocadx/trunk/ and has contributions from several members of the Debian Med team. -- System Information: Debian Release: squeeze/sid APT prefers oldstable APT policy: (500, 'oldstable'), (50, 'unstable') Architecture: i386 (i686) -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110527101342.12397.56651.report...@mail.an3as.eu
