Hi Sergei,
another reply in a couple of hours - thanks for beeing that responsive.
:-)
On Thu, Jul 09, 2015 at 09:48:22AM -0700, Sergei L Kosakovsky Pond wrote:
> I am copying our lead software engineer on this message so that he can help
> you out.
> We have moved the build system to CMAKE several years ago; please ensure you
> are using
> the latest release from github.com/veg/hyphy
I confirm that I'm talking about the latest release (version 2.2.4).
The R module build is not affected by the cmake build system and
requires an additional script.
> If you come across any issues in the build process, please report them on the
> project page
> (github.com/veg/hyphy), so there’s a record of their existence, and
> references to patches.
I'd happily open an issue un github - may be I'm waiting for a comment
from Simon to make it more qualified.
> As far as I recall, we don’t require .so files for standard binaries.
I can confirm that the executables run fine and the library does not
belong to the default build. However, if I build it than it is just
created and not used by the executables - so what is the purpose of the
library?
> I’ve also copied my colleague Simon Frost, who has motivated the development
> of the R
> library.
Thanks for forwarding
Andreas.
> >
> > Hi Andreas. Thanks for your interest in adding HyPhy to your list. I’m
> > copying Sergei Kosakovsky Pond, my collaborator who leads the HyPhy
> > implementation work. He should be able to answer your questions.
> >
> > Best wishes-
> > Spencer
> >
> > On Jul 9, 2015, at 7:34 AM, Andreas Tille <[email protected]> wrote:
> >
> >> Hi Spencer,
> >>
> >> I'm writing you on behalf of the Debian Med team which has the objective
> >> to package all relevant software for medicine and biology for the
> >> official Debian distribution. Since we received a request to package
> >> your program hyphy I have put it on our todo list[1]. I hope you are
> >> the correct contact person.
> >>
> >> I managed to build packages for hyphygtk and hyphympi. Since the test
> >> suite ran successfully I think these are OK and for the moment serve the
> >> need of the user asking for it. However, I have some more questions:
> >>
> >> What is the role of the dynamic library libhyphy_mp.so if I provide the
> >> LIB option to cmake? Usually in Debian it is good practice to do
> >> dynamic linking if possible but it seems the library exists simply for
> >> its own and the executables are statically linked. Could you please
> >> clarify this?
> >>
> >> I also tried to provide the python and R modules as well. Following
> >> src/lib/README I was calling
> >>
> >> sh build.sh LIBRARY R
> >>
> >> I noticed that this script requires Bash. If you want to run it using
> >> any POSIX shell (Debian is using Dash that is more simple an thus starts
> >> faster with a smaller memory footprint) please replase all "==" by "=".
> >> While this is no real problem in this case the script does not run since
> >> it seems to target at directory names of probably former versions of
> >> hyphy
> >>
> >>
> >> ...
> >> +-----------------------------------------------------------+
> >> |Building a multi-threaded HYPHY library version |
> >> +-----------------------------------------------------------+
> >> COMPILER=g++, gcc
> >> COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive
> >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../Core
> >>
> >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../NewerFunctionality
> >>
> >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../../SQLite/trunk
> >> -D SQLITE_PTR_SIZE=sizeof(long) -D __UNIX__ -D__HYPHY_NO_CURL__ -D
> >> __MP__ -D __MP2__ -D __HEADLESS__ -fPIC
> >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/Link
> >> -I
> >> /home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../Source
> >> build.sh: line 109: cd: ../Source: No such file or directory
> >> Building *cpp
> >> g++: error: *cpp: No such file or directory
> >> g++: fatal error: no input files
> >> compilation terminated.
> >>
> >>
> >> This is caused by by the following chunks in the script that lead to
> >> probably outdated directories:
> >>
> >>
> >> compileAll ../Source cpp ../Library
> >> compileAll ../GUI preferences.cpp ../Library
> >> compileAll ../Source/SQLite c ../../Library
> >>
> >>
> >> Since I do not like to wild guess I wonder whether you would be able to
> >> fix this script to enable R support for hyphy.
> >>
> >> The Python modules seem to be fine so far - I need to run the test suite
> >> on the final package, thought. I'll report in case of further problems
> >> in a separate mail.
> >>
> >> Kind regards and thanks for providing hyphy as free software
> >>
> >> Andreas.
> >>
> >> [1] http://blends.debian.org/med/tasks/bio#hyphy
> >>
> >> --
> >> http://fam-tille.de
> >
>
>
--
http://fam-tille.de
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