The cdd_both_reps/cdd_both_reps_gmp are used by the new polyhedra package, and are indeed introduced in cddlib-094f.p2.spkg.
I have no idea what the patches/allfaces.c is for - it does not part of the cddlib library, but only some utility binary. As far as I can tell the allfaces binary is never used by sage. Maybe whoever added it can shed some light on this? Its not documented in the SPKG.txt, sigh. As for the patches/cdd_both_reps-make.patch, this only records the changes to the automake source files. You still need to run autoconf/ automake to generate the makefiles from that. I still don't know the correct way of handling this: * The automake sources might be automake-version dependent. * Not everyone has all versions of automake installed, so spkg- install can't call automake. * Running autoconf/automake generates big shell scripts (configure, makefile). Differences in these need not be recorded. * But different versions of automake will produce different scripts, which would clutter up naive patches. See also: http://trac.sagemath.org/sage_trac/ticket/8079 I didn't realize that /src is supposed to be the pristine upstream source. Note that I previously entered a cddlib-094f.p3.spkg into trac for review at http://trac.sagemath.org/sage_trac/ticket/3304 to build cddlib as a shared library as well as a couple of other improvements. I'll try to merge the changes from your .p3 with mine and report back. Best wishes, Volker On Jan 29, 10:09 am, Minh Nguyen <nguyenmi...@gmail.com> wrote: > Hi folks, > > With Sage 4.3.2.alpha0, one has two suspicious binary files under > SAGE_LOCAL/bin, as shown by the following hg report: > > [mv...@sage bin]$ pwd > /dev/shm/mvngu/sage-4.3.2.alpha0-sage.math/local/bin > [mv...@sage bin]$ hg status > M sage-banner > M sage-gdb-commands > M sage-maxima.lisp > M sage-verify-pyc > ? cdd_both_reps > ? cdd_both_reps_gmp > > The files in question are cdd_both_reps and cdd_both_reps_gmp. It > turns out that these two files were put there by the package > cddlib-094f.p2.spkg. I think they were put there due to using the > command "patch" in spkg-install for patching the upstream source under > src/. > > A problem with cddlib-094f.p2.spkg is that it patches upstream source > using a patch file, rather than copying a patched file over to the > appropriate place under the src/ directory. Consequently, there is no > clean separation between upstream source and patches that we apply to > cddlib-094f. Looking at spkg-install of cddlib-094f.p2.spkg, you get > these two lines for applying Sage-specific patches: > > cp patches/allfaces.c src/src/ > > patch -p0 < patches/cdd_both_reps-make.patch > > The first line is the preferred way to patch an upstream source > because it copies the patched file patches/allfaces.c over to > src/src/. Even before running the installation script spkg-install, > the original upstream source is the file src/src/allfaces.c and its > corresponding patched version for Sage is patches/allfaces.c. And you > patch the upstream source using cp. In this way, you keep a clean > separation between the source provided by the upstream project and the > patches that the Sage project applies on top of the upstream source. > > Now let's consider the second line in the above code listing, i.e. > > patch -p0 < patches/cdd_both_reps-make.patch > > Patching an upstream source in this way results in modified upstream > source and this modification now lives under src/, which is supposedly > where the clean upstream source lives. Subsequently, anytime you want > to update (not upgrade to latest upstream release) the > cddlib-094f.p2.spkg package, you have modified source under src/. This > can cause a lot of confusion for maintainers who need to have a clean > separation between upstream source and Sage-specific patches. > > Here's an example illustrating that using the command "patch" in > spkg-install for patching upstream source is a bad idea. Say you have > a directory listing as follows: > > [mv...@sage cddlib]$ pwd > /home/mvngu/spkg/standard/cddlib > [mv...@sage cddlib]$ ls > cddlib-094f.p0 cddlib-094f.p0.spkg cddlib-094f.p2 cddlib-094f.p2.spkg > > In cddlib-094f.p2.spkg, the content of the file > patches/cdd_both_reps-make.patch is > > [mv...@sage cddlib]$ cat cddlib-094f.p2/patches/cdd_both_reps-make.patch > --- ../cddlib-094f/src/src-gmp/Makefile.am 2009-01-26 09:30:16.000000000 > +0000 > +++ src/src-gmp/Makefile.am 2009-10-04 10:36:17.000000000 +0100 > @@ -11,7 +11,8 @@ > testcdd2_gmp \ > testlp1_gmp \ > testlp2_gmp \ > -testlp3_gmp > +testlp3_gmp \ > +cdd_both_reps_gmp > #cddmathlink > > scdd_gmp_SOURCES = simplecdd.c > @@ -27,6 +28,7 @@ > testlp1_gmp_SOURCES = testlp1.c > testlp2_gmp_SOURCES = testlp2.c > testlp3_gmp_SOURCES = testlp3.c > +cdd_both_reps_gmp_SOURCES = cdd_both_reps.c > # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c > > LDADD = ../lib-src-gmp/libcddgmp.a > --- ../cddlib-094f/src/src/Makefile.am 2009-01-26 09:30:03.000000000 +0000 > +++ src/src/Makefile.am 2009-10-04 10:36:17.000000000 +0100 > @@ -11,7 +11,8 @@ > testcdd2 \ > testlp1 \ > testlp2 \ > -testlp3 > +testlp3 \ > +cdd_both_reps > #cddmathlink > > scdd_SOURCES = simplecdd.c > @@ -27,6 +28,7 @@ > testlp1_SOURCES = testlp1.c > testlp2_SOURCES = testlp2.c > testlp3_SOURCES = testlp3.c > +cdd_both_reps_SOURCES = cdd_both_reps.c > # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c > > LDADD = ../lib-src/libcdd.a > > Now compare cddlib-094f.p0/src/src-gmp/Makefile.am with > cddlib-094f.p2/src/src-gmp/Makefile.am and you'd get > > [mv...@sage cddlib]$ diff -u cddlib-094f.p0/src/src-gmp/Makefile.am > cddlib-094f.p2/src/src-gmp/Makefile.am--- > cddlib-094f.p0/src/src-gmp/Makefile.am 2009-01-26 01:30:16.000000000 > -0800 > +++ cddlib-094f.p2/src/src-gmp/Makefile.am 2009-10-15 13:25:26.000000000 > -0700 > @@ -11,7 +11,8 @@ > testcdd2_gmp \ > testlp1_gmp \ > testlp2_gmp \ > -testlp3_gmp > +testlp3_gmp \ > +cdd_both_reps_gmp > #cddmathlink > > scdd_gmp_SOURCES = simplecdd.c > @@ -27,6 +28,7 @@ > testlp1_gmp_SOURCES = testlp1.c > testlp2_gmp_SOURCES = testlp2.c > testlp3_gmp_SOURCES = testlp3.c > +cdd_both_reps_gmp_SOURCES = cdd_both_reps.c > # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c > > LDADD = ../lib-src-gmp/libcddgmp.a > > As you can see, cddlib-094f.p2.spkg is mashing up upstream source and > Sage-specific patch together and put the result under the directory > where the clean upstream, and only the clean upstream source, should > live. This is a recipe for confusion. An updated cddlib spkg is up at > > http://trac.sagemath.org/sage_trac/ticket/8115 > > awaiting review. On Sage 4.3.1, forcing a re-installation of the > updated cddlib spkg did not result in the above binary files copied > over to SAGE_LOCAL/bin. > > -- > Regards > Minh Van Nguyen -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
