Bug#868086: marked as done (RFS: beautify-bash/1.1-1 [ITP])

2017-11-28 Thread Debian Bug Tracking System 
Your message dated Wed, 29 Nov 2017 04:20:19 +
with message-id 
and subject line closing RFS: beautify-bash/1.1-1 [ITP]
has caused the Debian Bug report #868086,
regarding RFS: beautify-bash/1.1-1 [ITP]
to be marked as done.

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

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868086: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=868086
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--- Begin Message ---
Package: sponsorship-requests
Severity: wishlist

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

  Dear mentors,

  I am looking for a sponsor for my package "beautify-bash"

 * Package name: beautify-bash
   Version : 1.1-1
   Upstream Author : Paul Lutus, Shriram V 
 * URL : https://arachnoid.com/python/beautify_bash_program.html
 * License : GPL+
   Section : utils

  It builds those binary packages:

beautify-bash - Beautifier for Bash shell scripts written in Python

  To access further information about this package, please visit the following 
URL:

  https://mentors.debian.net/package/beautify-bash


  Alternatively, one can download the package with dget using this command:

dget -x 
https://mentors.debian.net/debian/pool/main/b/beautify-bash/beautify-bash_1.1-1.dsc

  Changes since the last upload:

beautify-bash (1.1-1) unstable; urgency=medium

  * Initial release (Closes: #867869)

 -- Mike Mestnik   Tue, 11 Jul 2017 13:21:00 
-0500

  Regards,
   Mike Mestnik

- --
Debian Release: 9.0
  APT prefers stable
  APT policy: (500, 'stable'), (480, 'unstable'), (470, 'experimental')
Architecture: i386 (x86_64)

Kernel: Linux 4.11.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

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--- Begin Message ---
Package beautify-bash has been removed from mentors.--- End Message ---

Re: CMake help needed to enable hdf5 for gatb-core (Was: [MoM] Re: gatb-core packaging)

2017-11-28 Thread Andreas Tille 
On Tue, Nov 28, 2017 at 10:00:48PM +0100, Christian Seiler wrote:
> Hi Andreas,
> 
> On 11/28/2017 11:52 AM, Andreas Tille wrote:
> > it turned out hat the cmake issue is a bit tricky for a MoM project so I
> > gave it a try myself.  The current state of gatb-core packaging is in
> > Git[1].  I went as far as my poor cmake knowledge permits to replace the
> > cmake hdf5 code to use the Debian packaged code after the internal code
> > copy was removed.  Unfortunately I failed to get the proper -I options
> > propagated to the compiler call since I'm ending up with:
> 
> Problem is that the system-wide hdf5.h  is always directly in the include
> path (#include , wherease the embedded code copy of the project
> you're trying to use was somehow put into the source project in such a
> way that they used #include  (see the error message). And
> since that _adds_ a directory layer, there's no -I flag you can pass that
> will make this work out of the box.
> 
> So you'll definitely need to patch the source files and replace
> #include  with #include 

I did so in
   
https://anonscm.debian.org/cgit/debian-med/gatb-core.git/tree/debian/patches/fix_hdf5_includes.patch

I guess this has no better effect than:

...
[  5%] Building CXX object 
src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o
cd /build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++   
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/include 
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/include/None 
-I/build/gatb-core-1.3.0+dfsg/gatb-core/src 
-I/build/gatb-core-1.3.0+dfsg/gatb-core/thirdparty  -g -O2 
-fdebug-prefix-map=/build/gatb-core-1.3.0+dfsg=. -fstack-protector-strong 
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 
-msse4.2 -mpopcnt   -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function 
-Wno-format -Wno-unknown-pragmas -Wno-invalid-offsetof -o 
CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp
cc1plus: error: -Wformat-security ignored without -Wformat 
[-Werror=format-security]
cc1plus: error: -Wformat-security ignored without -Wformat 
[-Werror=format-security]
cc1plus: error: -Wformat-security ignored without -Wformat 
[-Werror=format-security]
cc1plus: error: -Wformat-security ignored without -Wformat 
[-Werror=format-security]
In file included from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29:0,
 from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37,
 from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.hpp:31,
 from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp:20:
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:38:10: 
fatal error: hdf5.h: No such file or directory
 #include 
  ^~~~
cc1plus: some warnings being treated as errors
compilation terminated.
...


Since I also need to implement this ...

> Then you also have the problem that your compile line doesn't include
> the HDF5 directories. I haven't looked at your packaging, but in
> general you need to have the following in CMake to link against HDF5:
> 
> find_package(HDF5 REQUIRED)
> include_directories(${HDF5_INCLUDE_DIRS})
> target_link_libraries(name_of_program_or_library ${HDF5_LIBRARIES})
> 
> The last line possibly multiple times for multiple targets.

... properly.

I also added this to
   
https://anonscm.debian.org/cgit/debian-med/gatb-core.git/tree/debian/patches/use_debian_packaged_hdf5.patch
(line 60+) but I have no idea how to name the targets.  I'm sorry
but I'm quite illiterate in cmake and have no idea where to find
the proper location for this line and the target name. :-(

Sorry for requesting more detailed help.

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: CMake help needed to enable hdf5 for gatb-core (Was: [MoM] Re: gatb-core packaging)

2017-11-28 Thread Christian Seiler 
Hi Andreas,

On 11/28/2017 11:52 AM, Andreas Tille wrote:
> it turned out hat the cmake issue is a bit tricky for a MoM project so I
> gave it a try myself.  The current state of gatb-core packaging is in
> Git[1].  I went as far as my poor cmake knowledge permits to replace the
> cmake hdf5 code to use the Debian packaged code after the internal code
> copy was removed.  Unfortunately I failed to get the proper -I options
> propagated to the compiler call since I'm ending up with:

Problem is that the system-wide hdf5.h  is always directly in the include
path (#include , wherease the embedded code copy of the project
you're trying to use was somehow put into the source project in such a
way that they used #include  (see the error message). And
since that _adds_ a directory layer, there's no -I flag you can pass that
will make this work out of the box.

So you'll definitely need to patch the source files and replace
#include  with #include 

Then you also have the problem that your compile line doesn't include
the HDF5 directories. I haven't looked at your packaging, but in
general you need to have the following in CMake to link against HDF5:

find_package(HDF5 REQUIRED)
include_directories(${HDF5_INCLUDE_DIRS})
target_link_libraries(name_of_program_or_library ${HDF5_LIBRARIES})

The last line possibly multiple times for multiple targets.

Regards,
Christian

CMake help needed to enable hdf5 for gatb-core (Was: [MoM] Re: gatb-core packaging)

2017-11-28 Thread Andreas Tille 
Hi,

it turned out hat the cmake issue is a bit tricky for a MoM project so I
gave it a try myself.  The current state of gatb-core packaging is in
Git[1].  I went as far as my poor cmake knowledge permits to replace the
cmake hdf5 code to use the Debian packaged code after the internal code
copy was removed.  Unfortunately I failed to get the proper -I options
propagated to the compiler call since I'm ending up with:

...
[  5%] Building CXX object 
src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o
cd /build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++   
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/include 
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/ include/None 
-I/build/gatb-core-1.3.0+dfsg/gatb-core/src 
-I/build/gatb-core-1.3.0+dfsg/gatb-core/thirdparty  -g -O2 
-fdebug-prefix-map=/build/gatb-core-1.3.0+dfsg=. -fstack-protector-  strong 
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 
-msse4.2 -mpopcnt   -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function 
-Wno-format -Wno-unknown-pragmas -Wno- invalid-offsetof -o 
CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -c 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp
cd /build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++   
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/include 
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/ include/None 
-I/build/gatb-core-1.3.0+dfsg/gatb-core/src 
-I/build/gatb-core-1.3.0+dfsg/gatb-core/thirdparty  -g -O2 
-fdebug-prefix-map=/build/gatb-core-1.3.0+dfsg=. -fstack-protector-  strong 
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 
-msse4.2 -mpopcnt   -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function 
-Wno-format -Wno-unknown-pragmas -Wno- invalid-offsetof -o 
CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp
cc1plus: error: -Wformat-security ignored without -Wformat 
[-Werror=format-security]
cc1plus: error: -Wformat-security ignored without -Wformat 
[-Werror=format-security]
cc1plus: error: -Wformat-security ignored without -Wformat 
[-Werror=format-security]
In file included from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29:0,
 from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37,
 from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.hpp:31,
 from 
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp:20:
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:38:10: 
fatal error: hdf5/hdf5.h: No such file or directory
 #include 
  ^
cc1plus: some warnings being treated as errors
compilation terminated.
src/CMakeFiles/gatbcore-static.dir/build.make:137: recipe for target 
'src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o'
 failed
make[3]: *** 
[src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o]
 Error 1
...


Any help to use Debian packaged hdf5 would be really appreciated.

Kind regards

Andreas.


[1] https://anonscm.debian.org/git/debian-med/gatb-core.git

-- 
http://fam-tille.de