Re: Situs in Debian
Hi Mickaël,
I leave the full quote below because it was a long time ago when you
wrote the last time to Debian Med list. Did you got any response?
Do you have some preliminary packaging code for situs we might help
you somehow with? Do you managed to package other software on EMBL
in Grenoble?
Please be so kind to give some status report
Andreas.
On Tue, Jul 17, 2012 at 09:24:32AM +0200, Mickaël Canévet wrote:
> Hello,
>
> I'm writing you on behalf of the Debian Med project[1] which is a
> subproject of the Debian distribution targeting at making Debian the
> best distribution for medical care and bioinformatic research. I am
> interested in building an official Debian package of Situs. To do so, I
> had to do some adaptations to "debianize" it:
>
> - I fixed the install path so that it installs in $(DESTDIR)/usr/bin as
> expected by Debian (fix_install_path.patch)[2].
>
> - I fixed the clean and veryclean targets (fix_clean_targets.patch)
> because the clean target should work in any case and your one does not
> if you don't have launch a 'make all' first and the veryclean target
> deletes files included in the archive (binaries) and should not.
> Anyway, could you ship without any pre-compiled binaries to simplify
> this (you could possibly provide these in separate downloadable
> tarball) ?
>
> - I had to patch Makefile to link towards libfftw provided by the system
> instead of the one you provides (fix_libfftw_link.patch).
> I think it would be great if you would at least provide a simple
> method (variable you could pass to make to simply ignore the convenience
> copy of the libfftw library). It would even be better to make it the
> default to use system libraries if these are found. Or even don't
> provide the libfftw at all and specify the requirement in the
> installation doc.
>
> Also, to download the source I ended up with some download page[3]. I
> know that there might be reasons for you to control the number of
> downloads but this on one hand disables our tools[4] to reasonably
> detect new version numbers and on the other hand a packaging for Debian
> means that the source tarball will be available on a different place
> than yours. The reward we could give is real user numbers via popcon[5]
> results.
>
> Thanks in advance for any help and feel free to ask back for any
> clarification if needed.
>
> Mickaël Canévet
>
> [1] http://www.debian.org/devel/debian-med
> [2] http://www.gnu.org/prep/standards/html_node/DESTDIR.html
> [3] http://situs.biomachina.org/freg1.html
> [4] http://wiki.debian.org/debian/watch/
> [5] http://popcon.debian.org/
> Description: Fix clean and veryclean target.
> Author: Mickaël Canévet <canevet@embl.fr>
> Forwarded: no
> Last-update: 2012-07-16
> --- a/src/Makefile
> +++ b/src/Makefile
> @@ -171,11 +171,10 @@
>
> clean:
> $(RM) $(OBJ_FILES)
> - $(MV) $(SITUS_EXEC) $(BIN_DIR)
> + $(RM) $(SITUS_EXEC)
>
> veryclean:
> $(RM) $(OBJ_FILES)
> - $(CD) $(BIN_DIR) && $(RM) $(SITUS_EXEC)
>
> .c.o:
> $(CC) $(CFLAGS) $(SMP) $(OMP) -c $(SRC_DIR)/$<
> Description: Use $(DESTDIR)/usr/bin as install path instead of ../bin
> Author: Mickaël Canévet <canevet@embl.fr>
> Forwarded: no
> Last-update: 2012-07-16
> --- a/src/Makefile
> +++ b/src/Makefile
> @@ -3,7 +3,7 @@
> #####
>
> SRC_DIR = .
> -BIN_DIR = ../bin
> +BIN_DIR = $(DESTDIR)/usr/bin
> SHELL = /bin/sh
>
> #####
> @@ -166,7 +166,8 @@
> $(RANLIB) libfftw.a
>
> install:
> - $(MV) $(SITUS_EXEC) $(BIN_DIR)
> + mkdir -p $(BIN_DIR)
> + install $(SITUS_EXEC) $(BIN_DIR)
>
> clean:
> $(RM) $(OBJ_FILES)
> Description: Build towards distribution's libfftw
> Author: Mickaël Canévet <canevet@embl.fr>
> Forwarded: no
> Last-update: 2012-07-16
> --- a/src/Makefile
> +++ b/src/Makefile
> @@ -17,7 +17,7 @@
> # any extra compiler and linker options (see the compiler man page)
> #####
>
> -CFLAGS = -O3 -w -I../fftw
> +CFLAGS = -O3 -w
> XFLAGS = -O3 -w
> LFLAGS = -lm
>
> @@ -53,15 +53,7 @@
>
> SITUS_EXEC = $(SITUS_C:.c=) $(SITUS_CPP:.cpp=)
>
> -#####
> -# FFTW files
> -#####
> -
> -FFTWCFILES = $(wildcard ../fftw/*.c)
> -FFTWOFILES = $(patsubst %.c,%.o,$(notdir $(FFTWCFILES)))
> -
> vpath %.c $(SRC_DIR)
> -vpath %.c ../fftw
>
> AR = ar
> ARFLAGS = cru
> @@ -74,7 +66,7 @@
> CD = cd
> RM = rm -f
> MV = mv
> -OBJ_FILES = $(wildcard *.o) libfftw.a
> +OBJ_FILES = $(wildcard *.o)
>
> #####
> # main makefile rules
> @@ -129,8 +121,8 @@
> collage: collage.o lib_std.o lib_pio.o lib_vwk.o lib_vec.o lib_rnd.o lib_pwk.o lib_pow.o lib_err.o lib_eul.o lib_tim.o lib_smp.o lib_vio.o
> $(CC) collage.o lib_std.o lib_pio.o lib_vio.o lib_vwk.o lib_vec.o lib_rnd.o lib_pwk.o lib_pow.o lib_err.o lib_eul.o lib_tim.o lib_smp.o $(LFLAGS) $(SMPLIB) -o collage
>
> -colores: colores.o lib_std.o lib_pio.o lib_vwk.o lib_vec.o lib_rnd.o lib_pwk.o lib_pow.o lib_err.o lib_eul.o lib_tim.o lib_smp.o lib_vio.o libfftw.a
> - $(CC) colores.o lib_std.o lib_pio.o lib_vio.o lib_vwk.o lib_vec.o lib_rnd.o lib_pwk.o lib_pow.o lib_err.o lib_eul.o lib_tim.o lib_smp.o libfftw.a $(LFLAGS) $(SMPLIB) $(OMPLIB) -o colores
> +colores: colores.o lib_std.o lib_pio.o lib_vwk.o lib_vec.o lib_rnd.o lib_pwk.o lib_pow.o lib_err.o lib_eul.o lib_tim.o lib_smp.o lib_vio.o
> + $(CC) colores.o lib_std.o lib_pio.o lib_vio.o lib_vwk.o lib_vec.o lib_rnd.o lib_pwk.o lib_pow.o lib_err.o lib_eul.o lib_tim.o lib_smp.o $(LFLAGS) $(SMPLIB) $(OMPLIB) -lfftw -lrfftw -o colores
>
> matchpt: matchpt.o lib_mpt.o
> $(CXX) $(CFLAGS) -c lib_err.c
> @@ -161,10 +153,6 @@
> $(CXX) volfltr.o lib_sba.o lib_svt.o lib_vio.o lib_vwk.o lib_vec.o lib_std.o lib_err.o $(LFLAGS) $(OMPLIB) $(SMPLIB) -o volfltr
> $(RM) lib_vio.o lib_vwk.o lib_vec.o lib_std.o lib_err.o
>
> -libfftw.a: $(FFTWOFILES)
> - $(AR) $(ARFLAGS) libfftw.a $(FFTWOFILES)
> - $(RANLIB) libfftw.a
> -
> install:
> mkdir -p $(BIN_DIR)
> install $(SITUS_EXEC) $(BIN_DIR)
--
http://fam-tille.de
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