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
