Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-11 Thread Maarten L. Hekkelman 

Hi Juhani,

Bug #974074 is in fact a bug in MRS. However, the bug report does 
contain a useful observation, the usage of the various 
override_dh_auto_configure rules in libzeep is incorrect and no shared 
library is created.


Now the question is, is a shared library really required? If so I will 
have to go back to the drawing board and redesign the makefiles in the 
upstream project to create proper shared libraries, including a version 
numbering scheme.


regards, -maarten


Op 11-11-2020 om 09:13 schreef Juhani Numminen:

On Tue, 10 Nov 2020 23:03:57 +0100 Sebastian Ramacher  
wrote:

Hi Marten

On 2020-11-10 07:42:45 +0100, Maarten L. Hekkelman wrote:
...

Sorry, long story. To make it short.
- Keep mrc, no problem there
- Upgrade libzeep to version 5


Thanks for the detailed explanation. The first two steps are almost done
The current versions of mrc and libzeep should be able to migrate soon
as their RC bugs have been fixed.
...

Right, but one RC bug is not fixed yet: libzeep packages are missing the
shared library altogether; the .so files are not there.

For that we have bug #974074, and see gregor's message for suggested fix.
It seems he is confident in the first diff of that mail, while the latter diff
is more speculative.
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974074#19


Regards,
Juhani




--
Maarten L. Hekkelman
Cataloniëstraat 3
6663NJ Lent

http://www.hekkelman.com/
+31 24 348 0192

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-11 Thread Andreas Tille 
On Wed, Nov 11, 2020 at 11:09:32AM +0100, Maarten L. Hekkelman wrote:
> Hi Juhani,
> 
> Bug #974074 is in fact a bug in MRS. However, the bug report does contain a
> useful observation, the usage of the various override_dh_auto_configure
> rules in libzeep is incorrect and no shared library is created.
> 
> Now the question is, is a shared library really required?

Yes, definitely.

> If so I will have
> to go back to the drawing board and redesign the makefiles in the upstream
> project to create proper shared libraries, including a version numbering
> scheme.

Usually a library package should feature both:  Shared is mandatory and
static recommended.  The shared library should have a proper SOVERSION.

Kind regards

   Andreas.

> regards, -maarten
> 
> 
> Op 11-11-2020 om 09:13 schreef Juhani Numminen:
> > On Tue, 10 Nov 2020 23:03:57 +0100 Sebastian Ramacher 
> >  wrote:
> > > Hi Marten
> > > 
> > > On 2020-11-10 07:42:45 +0100, Maarten L. Hekkelman wrote:
> > > ...
> > > > Sorry, long story. To make it short.
> > > > - Keep mrc, no problem there
> > > > - Upgrade libzeep to version 5
> > > > 
> > > Thanks for the detailed explanation. The first two steps are almost done
> > > The current versions of mrc and libzeep should be able to migrate soon
> > > as their RC bugs have been fixed.
> > > ...
> > Right, but one RC bug is not fixed yet: libzeep packages are missing the
> > shared library altogether; the .so files are not there.
> > 
> > For that we have bug #974074, and see gregor's message for suggested fix.
> > It seems he is confident in the first diff of that mail, while the latter 
> > diff
> > is more speculative.
> > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974074#19
> > 
> > 
> > Regards,
> > Juhani
> > 
> > 
> 
> -- 
> Maarten L. Hekkelman
> Cataloniëstraat 3
> 6663NJ Lent
> 
> http://www.hekkelman.com/
> +31 24 348 0192
> 
> 

-- 
http://fam-tille.de

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-11 Thread Juhani Numminen 
On Tue, 10 Nov 2020 23:03:57 +0100 Sebastian Ramacher  
wrote:
> Hi Marten
> 
> On 2020-11-10 07:42:45 +0100, Maarten L. Hekkelman wrote:
> ...
> > 
> > Sorry, long story. To make it short.
> > - Keep mrc, no problem there
> > - Upgrade libzeep to version 5
> >
> 
> Thanks for the detailed explanation. The first two steps are almost done
> The current versions of mrc and libzeep should be able to migrate soon
> as their RC bugs have been fixed.
> ...

Right, but one RC bug is not fixed yet: libzeep packages are missing the
shared library altogether; the .so files are not there.

For that we have bug #974074, and see gregor's message for suggested fix.
It seems he is confident in the first diff of that mail, while the latter diff
is more speculative.
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974074#19


Regards,
Juhani

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-10 Thread Sebastian Ramacher 
Hi Marten

On 2020-11-10 07:42:45 +0100, Maarten L. Hekkelman wrote:
> Hi Andreas,
> 
> To avoid confusion, we're talking about three tools here: libzeep, mrc and
> mrs.
> 
> mrc is a simple resource compiler, is now compatible and bug free, builds on
> all architectures and should be kept. I believe it is very useful, using it
> I can create downloadable, portable applications that need additional static
> data without the need for installer scripts.
> 
> libzeep version 5 is the latest incarnation of a library I've been working
> on for 12 years now. It has evolved into a toolbox to build web applications
> in C++ inspired by the popular Java Spring framework and Thymeleaf template
> processor. It also contains a full XML and a JSON library. Using this
> library I could e.g. convert a pipeline to process genomics data into an
> interactive web application, the python scripts took up to 4 hours for each
> run, now you can do the same analysis in less than 5 seconds. I have a
> couple of applications based on libzeep that I would like to add to Debian,
> most of them tools used in crystallography and genomics research. But also a
> content management system.
> 
> And then we have MRS. This is a retrieval system, a web application capable
> of indexing and then searching terabytes of text based databanks on a single
> machine. Mostly used in the medical and biological world. It is used e.g. on
> mini computers that are sent into Africa where internet access is limited,
> that way large databanks like EMBL are still available. But I stopped
> development in 2012 when I switched jobs. I continued development of libzeep
> on which MRS is based but someone else took over development of MRS. A year
> ago I did a consultancy job fixing MRS which basically came down to
> reverting most of the attempted 'improvements' after I left.
> 
> Currently I'm working at the Netherlands Cancer Institute, here I write both
> software used in crystallography as well as a genomics analysis tool. Many
> of the crystallographic tools are moving into open source right now. We
> would have liked to include those in the CCP4 distribution, but
> unfortunately my code is way too new (C++17) to work in that environment.
> Next to that we would like to include our tools in Debian (DSSP already is,
> but that application needs an update), but if that won't work, I will set up
> a private repository to distribute our binaries.
> 
> I know libzeep is not very popular, that's because I never bothered much to
> find an audience. But I can't live without it myself, a lot of my tools are
> based on it one way or another. Libzeep is also quite mature and has been
> used in many tools in a production environment for many years now.
> 
> Sorry, long story. To make it short.
> - Keep mrc, no problem there
> - Upgrade libzeep to version 5
> - Kick out mrs until it is upgraded to use libzeep 5

Thanks for the detailed explanation. The first two steps are almost done
The current versions of mrc and libzeep should be able to migrate soon
as their RC bugs have been fixed.  I've now added a removal hint to
remove mrs from testing to complete the last step.

Cheers
-- 
Sebastian Ramacher


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Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-10 Thread Maarten L. Hekkelman 

Hi Andreas,

To avoid confusion, we're talking about three tools here: libzeep, mrc 
and mrs.


mrc is a simple resource compiler, is now compatible and bug free, 
builds on all architectures and should be kept. I believe it is very 
useful, using it I can create downloadable, portable applications that 
need additional static data without the need for installer scripts.


libzeep version 5 is the latest incarnation of a library I've been 
working on for 12 years now. It has evolved into a toolbox to build web 
applications in C++ inspired by the popular Java Spring framework and 
Thymeleaf template processor. It also contains a full XML and a JSON 
library. Using this library I could e.g. convert a pipeline to process 
genomics data into an interactive web application, the python scripts 
took up to 4 hours for each run, now you can do the same analysis in 
less than 5 seconds. I have a couple of applications based on libzeep 
that I would like to add to Debian, most of them tools used in 
crystallography and genomics research. But also a content management system.


And then we have MRS. This is a retrieval system, a web application 
capable of indexing and then searching terabytes of text based databanks 
on a single machine. Mostly used in the medical and biological world. It 
is used e.g. on mini computers that are sent into Africa where internet 
access is limited, that way large databanks like EMBL are still 
available. But I stopped development in 2012 when I switched jobs. I 
continued development of libzeep on which MRS is based but someone else 
took over development of MRS. A year ago I did a consultancy job fixing 
MRS which basically came down to reverting most of the attempted 
'improvements' after I left.


Currently I'm working at the Netherlands Cancer Institute, here I write 
both software used in crystallography as well as a genomics analysis 
tool. Many of the crystallographic tools are moving into open source 
right now. We would have liked to include those in the CCP4 
distribution, but unfortunately my code is way too new (C++17) to work 
in that environment. Next to that we would like to include our tools in 
Debian (DSSP already is, but that application needs an update), but if 
that won't work, I will set up a private repository to distribute our 
binaries.


I know libzeep is not very popular, that's because I never bothered much 
to find an audience. But I can't live without it myself, a lot of my 
tools are based on it one way or another. Libzeep is also quite mature 
and has been used in many tools in a production environment for many 
years now.


Sorry, long story. To make it short.
- Keep mrc, no problem there
- Upgrade libzeep to version 5
- Kick out mrs until it is upgraded to use libzeep 5

regards, -maarten

Op 09-11-2020 om 20:49 schreef Andreas Tille:

Hi Maarten,

On Mon, Nov 09, 2020 at 07:22:30PM +0100, Maarten L. Hekkelman wrote:

I'm sorry, but mrs as it is currently in Debian is not compatible with
libzeep version 5. It needs a major rewrite. Libzeep is a spin off project
of mrs and has evolved a lot since then.

So either libzeep should be kept at version 3 or mrs should be removed. If
mrs and libzeep are kept, I will not be able to release my other tools based
on libzeep in Debian.

You are the Uploader and the only competent person to decide.  If I
understood the issue correctly it came up right after mrc was added to
the Build-Depends.  Wouldn't it be an option to just de-couple both
again.
  

Upgrading mrs is of course the best option, but I won't have time to do that
soon.

So please draw a sensible decision.  Libzeep was according to popcon[1]
never installed by more than 10 users - currently the vote (active users)
is at zero.  Feel free to decided what *you* personally love to see in
Debian (but decreasing a version number is usually not nice).

Kind regards

  Andreas.

[1] https://qa.debian.org/popcon.php?package=libzeep
  

regards, -maarten

Op 09-11-2020 om 16:19 schreef Niko Tyni:

On Mon, Nov 09, 2020 at 09:17:25AM +0200, Juhani Numminen wrote:

Source: mrs
Version: 6.0.5+dfsg-8
Severity: serious
Tags: ftbfs sid
Justification: fails to build from source (but built successfully in the past)
| Checking for libzeep...libzeep is not installed, either install the package 
libzeep-dev
| or download libzeep from ftp://ftp.cmbi.ru.nl/pub/software/libzeep
| and run configure again.
| make[1]: *** [debian/rules:15: override_dh_auto_configure] Error 2

Looks to me like libzeep-dev is broken because the build
doesn't pass --enable-shared to ./configure.

Probably the override_dh_auto_configure-arch and
override_dh_auto_configure-indep targets in src:libzeep debian/rules
are not effective because of the earlier override_dh_auto_configure
target. But I didn't actually test any of this.

Hope this helps,

--
Maarten L. Hekkelman
Cataloniëstraat 3
6663NJ Lent

http://www.hekkelman.com/



--
Maarten L. Hekkelman
Cataloniëstraat 3
6663NJ Lent

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-10 Thread gregor herrmann 
On Tue, 10 Nov 2020 08:18:27 +0100, Andreas Tille wrote:

> On Tue, Nov 10, 2020 at 07:42:45AM +0100, Maarten L. Hekkelman wrote:
> > Sorry, long story. To make it short.
> > - Keep mrc, no problem there
> > - Upgrade libzeep to version 5

libzeep is already at version 5 in unstable but has some issues:
https://tracker.debian.org/pkg/libzeep
https://bugs.debian.org/src:libzeep

> > - Kick out mrs until it is upgraded to use libzeep 5
> I'd recommend to file an RC critical bug against mrs and give some
> explanation (may be by simply copying the relevant parts of your
> explanation.)  

Adding this explanations would indeed be helpful, besides that, mrs
already has one RC bug:

https://tracker.debian.org/pkg/mrs
https://bugs.debian.org/974016


Cheers,
gregor

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Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-09 Thread Andreas Tille 
Hi Maarten,

On Tue, Nov 10, 2020 at 07:42:45AM +0100, Maarten L. Hekkelman wrote:
> ...

Thanks a lot for the explanation.

> Sorry, long story. To make it short.
> - Keep mrc, no problem there
> - Upgrade libzeep to version 5
> - Kick out mrs until it is upgraded to use libzeep 5

I'd recommend to file an RC critical bug against mrs and give some
explanation (may be by simply copying the relevant parts of your
explanation.)  This will prevent it from beeing included into the
next stable release.  If you think its better to remove it completely
from Debian file a ROM bug (Request Of Removal) via

 reportbug other

and select ftpmaster (I think its number 11) and continue the
menu to remove it fully from Debian.

Kind regards

   Andreas.

-- 
http://fam-tille.de

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-09 Thread Maarten L. Hekkelman 
I'm sorry, but mrs as it is currently in Debian is not compatible with 
libzeep version 5. It needs a major rewrite. Libzeep is a spin off 
project of mrs and has evolved a lot since then.


So either libzeep should be kept at version 3 or mrs should be removed. 
If mrs and libzeep are kept, I will not be able to release my other 
tools based on libzeep in Debian.


Upgrading mrs is of course the best option, but I won't have time to do 
that soon.


regards, -maarten

Op 09-11-2020 om 16:19 schreef Niko Tyni:

On Mon, Nov 09, 2020 at 09:17:25AM +0200, Juhani Numminen wrote:

Source: mrs
Version: 6.0.5+dfsg-8
Severity: serious
Tags: ftbfs sid
Justification: fails to build from source (but built successfully in the past)
| Checking for libzeep...libzeep is not installed, either install the package 
libzeep-dev
| or download libzeep from ftp://ftp.cmbi.ru.nl/pub/software/libzeep
| and run configure again.
| make[1]: *** [debian/rules:15: override_dh_auto_configure] Error 2

Looks to me like libzeep-dev is broken because the build
doesn't pass --enable-shared to ./configure.

Probably the override_dh_auto_configure-arch and
override_dh_auto_configure-indep targets in src:libzeep debian/rules
are not effective because of the earlier override_dh_auto_configure
target. But I didn't actually test any of this.

Hope this helps,


--
Maarten L. Hekkelman
Cataloniëstraat 3
6663NJ Lent

http://www.hekkelman.com/

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-09 Thread Andreas Tille 
Hi Maarten,

On Mon, Nov 09, 2020 at 07:22:30PM +0100, Maarten L. Hekkelman wrote:
> I'm sorry, but mrs as it is currently in Debian is not compatible with
> libzeep version 5. It needs a major rewrite. Libzeep is a spin off project
> of mrs and has evolved a lot since then.
> 
> So either libzeep should be kept at version 3 or mrs should be removed. If
> mrs and libzeep are kept, I will not be able to release my other tools based
> on libzeep in Debian.

You are the Uploader and the only competent person to decide.  If I
understood the issue correctly it came up right after mrc was added to
the Build-Depends.  Wouldn't it be an option to just de-couple both
again.
 
> Upgrading mrs is of course the best option, but I won't have time to do that
> soon.

So please draw a sensible decision.  Libzeep was according to popcon[1]
never installed by more than 10 users - currently the vote (active users)
is at zero.  Feel free to decided what *you* personally love to see in
Debian (but decreasing a version number is usually not nice).

Kind regards

 Andreas.

[1] https://qa.debian.org/popcon.php?package=libzeep
 
> regards, -maarten
> 
> Op 09-11-2020 om 16:19 schreef Niko Tyni:
> > On Mon, Nov 09, 2020 at 09:17:25AM +0200, Juhani Numminen wrote:
> > > Source: mrs
> > > Version: 6.0.5+dfsg-8
> > > Severity: serious
> > > Tags: ftbfs sid
> > > Justification: fails to build from source (but built successfully in the 
> > > past)
> > > | Checking for libzeep...libzeep is not installed, either install the 
> > > package libzeep-dev
> > > | or download libzeep from ftp://ftp.cmbi.ru.nl/pub/software/libzeep
> > > | and run configure again.
> > > | make[1]: *** [debian/rules:15: override_dh_auto_configure] Error 2
> > Looks to me like libzeep-dev is broken because the build
> > doesn't pass --enable-shared to ./configure.
> > 
> > Probably the override_dh_auto_configure-arch and
> > override_dh_auto_configure-indep targets in src:libzeep debian/rules
> > are not effective because of the earlier override_dh_auto_configure
> > target. But I didn't actually test any of this.
> > 
> > Hope this helps,
> 
> -- 
> Maarten L. Hekkelman
> Cataloniëstraat 3
> 6663NJ Lent
> 
> http://www.hekkelman.com/
> 

-- 
http://fam-tille.de

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-09 Thread gregor herrmann 
Control: clone -1 -2
Control: reassign -2 src:libzeep 5.0.0-1
Control: retitle -2 "src:libzeep: override targets never called"
Control: block -1 with -2

On Mon, 09 Nov 2020 15:19:21 +, Niko Tyni wrote:

> Looks to me like libzeep-dev is broken because the build
> doesn't pass --enable-shared to ./configure.
> 
> Probably the override_dh_auto_configure-arch and
> override_dh_auto_configure-indep targets in src:libzeep debian/rules
> are not effective because of the earlier override_dh_auto_configure
> target. But I didn't actually test any of this.

This sounds very plausible to me after a quick check:


For arch-dependent packages:

% dh binary --no-act -a | grep configure
   debian/rules override_dh_auto_configure

For arch-independent packages:

% dh binary --no-act -i | grep configure 
   debian/rules override_dh_auto_configure


I.e. both override_dh_auto_configure-arch and
override_dh_auto_configure-indep are never called.

(The's also what the build logs show. Only
override_dh_auto_configure.)


With the following change

#v+
--- debian/rules.orig   2020-11-09 17:21:31.564290254 +0100
+++ debian/rules2020-11-09 17:21:59.816434767 +0100
@@ -12,9 +12,6 @@
 %:
dh $@
 
-override_dh_auto_configure:
-   dh_auto_configure -- --enable-documentation
-
 override_dh_auto_install:
$(MAKE) DESTDIR=$(CURDIR)/debian/libzeep5.0 install-libs
$(MAKE) DESTDIR=$(CURDIR)/debian/libzeep-dev install-dev
@@ -24,7 +21,7 @@
dh_auto_configure -- --enable-shared --disable-documentation
 
 override_dh_auto_configure-indep:
-   dh_auto_configure -- --enable-shared
+   dh_auto_configure -- --enable-shared --enable-documentation
 
 override_dh_auto_build-indep:
cd $(CURDIR)/doc/ && bjam
#v-

this looks much better:


% dh binary --no-act -a | grep configure
   debian/rules override_dh_auto_configure-arch

% dh binary --no-act -i | grep configure 
   debian/rules override_dh_auto_configure-indep


Not sure which combination of flags in which override target is
actually needed/useful. Maybe the following also works:

#v+
--- debian/rules.orig   2020-11-09 17:21:31.564290254 +0100
+++ debian/rules2020-11-09 17:27:26.694107367 +0100
@@ -12,19 +12,13 @@
 %:
dh $@
 
-override_dh_auto_configure:
-   dh_auto_configure -- --enable-documentation
-
 override_dh_auto_install:
$(MAKE) DESTDIR=$(CURDIR)/debian/libzeep5.0 install-libs
$(MAKE) DESTDIR=$(CURDIR)/debian/libzeep-dev install-dev
$(MAKE) DESTDIR=$(CURDIR)/debian/libzeep-doc install-doc
 
-override_dh_auto_configure-arch:
-   dh_auto_configure -- --enable-shared --disable-documentation
-
 override_dh_auto_configure-indep:
-   dh_auto_configure -- --enable-shared
+   dh_auto_configure -- --enable-documentation
 
 override_dh_auto_build-indep:
cd $(CURDIR)/doc/ && bjam
#v-

% dh binary --no-act -a | grep configure
   dh_auto_configure -O-a

% dh binary --no-act -i | grep configure 
   debian/rules override_dh_auto_configure-indep


Cloning/reassigning. mrs should probably build-depend on a fixed
libzeep afterwards.



Cheers,
gregor

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Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-09 Thread Niko Tyni 
On Mon, Nov 09, 2020 at 09:17:25AM +0200, Juhani Numminen wrote:
> Source: mrs
> Version: 6.0.5+dfsg-8
> Severity: serious
> Tags: ftbfs sid
> Justification: fails to build from source (but built successfully in the past)

> | Checking for libzeep...libzeep is not installed, either install the package 
> libzeep-dev
> | or download libzeep from ftp://ftp.cmbi.ru.nl/pub/software/libzeep
> | and run configure again.
> | make[1]: *** [debian/rules:15: override_dh_auto_configure] Error 2

Looks to me like libzeep-dev is broken because the build
doesn't pass --enable-shared to ./configure.

Probably the override_dh_auto_configure-arch and
override_dh_auto_configure-indep targets in src:libzeep debian/rules
are not effective because of the earlier override_dh_auto_configure
target. But I didn't actually test any of this.

Hope this helps,
-- 
Niko Tyni   nt...@debian.org

Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

2020-11-08 Thread Juhani Numminen 
Source: mrs
Version: 6.0.5+dfsg-8
Severity: serious
Tags: ftbfs sid
Justification: fails to build from source (but built successfully in the past)

Dear Maintainer,

mrs fails to build from source on multiple architectures, with the message
quoted below. See .

| ./configure --prefix=/usr --config-dir=/etc/mrs/ \
|   --man-dir=/usr/share/man --mrs-user=mrs-dba \
|   --data-dir=/var/lib/mrs --log-dir=/var/log/mrs
| length() used on @boost_version (did you mean "scalar(@boost_version)"?) at 
./configure line 289.
| Using perl /usr/bin/perl
| Checking for a compiler... OK
| Checking for libboost... OK
| Checking for libzeep...libzeep is not installed, either install the package 
libzeep-dev
| or download libzeep from ftp://ftp.cmbi.ru.nl/pub/software/libzeep
| and run configure again.
| make[1]: *** [debian/rules:15: override_dh_auto_configure] Error 2


--
Juhani