Re: Problem creating R module in hyphy
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 <andreas@an3as.eu> 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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