Problem creating R module in hyphy
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probably outdated directories: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
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