[Debian-med-packaging] Bug#974016: mrs: FTBFS with libzeep-dev 5.0.0-1: "Checking for libzeep...libzeep is not installed"

Tue Nov 10 06:42:45 GMT 2020

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

http://www.hekkelman.com/

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