Aaron M. Ucko pushed to branch master at Debian Med / ncbi-igblast
Commits: 7f9c4ebe by Aaron M. Ucko at 2023-01-20T17:06:42-05:00 avoid-gcc-crash.patch (new): Work around a consistent ICE ... whose fix may run into the toolchain freeze: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=108137 - - - - - cdaf8ca5 by Aaron M. Ucko at 2023-01-20T17:12:49-05:00 debian/rules: Add possibly relevant subtrees to VDB_INCLUDE. - - - - - 3ea3684a by Aaron M. Ucko at 2023-01-20T17:14:51-05:00 Enable optimization unless DEB_BUILD_OPTIONS contains noopt. - - - - - 5dbd0ce5 by Aaron M. Ucko at 2023-01-20T17:20:23-05:00 debian/rules: Copy-hack clean logic from ncbi-blast+. - - - - - 4 changed files: - debian/changelog - + debian/patches/avoid-gcc-crash.patch - + debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,6 @@ ncbi-igblast (1.20.0-1) UNRELEASED; urgency=medium + [ Andreas Tille ] * Team upload. * Fix lintian-overrides * Recommends: ncbi-blast+ @@ -10,7 +11,16 @@ ncbi-igblast (1.20.0-1) UNRELEASED; urgency=medium * Update lintian override info format in d/source/lintian-overrides on line 4-6. - -- Andreas Tille <[email protected]> Sat, 30 Jul 2022 09:29:11 +0200 + [ Aaron M. Ucko ] + * debian/patches/avoid-gcc-crash.patch (new): Work around a consistent + internal compiler error whose fix may run into the toolchain freeze: + https://gcc.gnu.org/bugzilla/show_bug.cgi?id=108137 + * debian/rules: + - Add possibly relevant subtrees to VDB_INCLUDE. + - Enable optimization unless DEB_BUILD_OPTIONS contains noopt. + - Copy-hack clean logic from ncbi-blast+. + + -- Aaron M. Ucko <[email protected]> Fri, 20 Jan 2023 17:20:22 -0500 ncbi-igblast (1.19.0-1) unstable; urgency=medium ===================================== debian/patches/avoid-gcc-crash.patch ===================================== @@ -0,0 +1,18 @@ +Index: b/c++/src/connect/ncbi_socket.c +=================================================================== +--- a/c++/src/connect/ncbi_socket.c ++++ b/c++/src/connect/ncbi_socket.c +@@ -6037,11 +6037,12 @@ static EIO_Status s_SendMsg(SOCK + + if (!x_host || !x_port) { + SOCK_HostPortToString(x_host, x_port, w, sizeof(w)/2); ++ const char* missing = x_port ? "host" : &"host:port"[x_host ? 5 : 0]; + CORE_LOGF_X(89, eLOG_Error, + ("%s[DSOCK::SendMsg] " + " Address \"%s\" incomplete, missing %s", + s_ID(sock, w + sizeof(w)/2), w, +- x_port ? "host" : &"host:port"[x_host ? 5 : 0])); ++ missing)); + return eIO_Unknown; + } + if (s_ApproveHook) { ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +avoid-gcc-crash.patch ===================================== debian/rules ===================================== @@ -3,11 +3,19 @@ %: dh $@ --sourcedirectory=c++ +ifeq(,$(filter noopt,$(DEB_BUILD_OPTIONS))) + WITH_OPTIM=--with-optimization +endif + +VDB_SUBTREES=os/$(DEB_HOST_ARCH_OS) os/unix cc/gcc/$(DEB_HOST_GNU_CPU) cc/gcc +VDB_INC=-I/usr/include/ncbi-vdb +VDB_INCLUDE=$(VDB_INC) $(VDB_SUBTREES:%=$(VDB_INC)/%) + override_dh_auto_configure: cd c++ && yes | \ ./configure.orig --prefix=/usr \ - --with-openmp \ - --with-vdb=/usr VDB_INCLUDE=-I/usr/include/ncbi-vdb \ + --with-openmp $(WITH_OPTIM) \ + --with-vdb=/usr VDB_INCLUDE="$(VDB_INCLUDE)" \ --without-runpath \ --with-flat-makefile @@ -22,5 +30,20 @@ override_dh_auto_install: override_dh_clean: # cleans *.orig files, which it should not - rm -fr ./c++/GCC1020-ReleaseDLL64 dh_clean -X*.orig + #Tricky - for each module directory there may be several module files + #or there may be none but then there is still a module named after the + #directory. Clean everything! + -for x in c++/src/objects/* ; do \ + (cd "$$x" && ( \ + mods="`echo *.module`" ; \ + [ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \ + for mod in $$mods ; do \ + ../../../GCC*/build/new_module.sh $$mod \ + purge_sources ; \ + done ) ; \ + ) ; \ + done + rm -rf c++/compilers/dll c++/config.log c++/Makefile c++/GCC* + rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module + rm -f c++/include/common/ncbi_revision.h View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/f1b140f84d26166d4fa75eb072276a3a118f092d...5dbd0ce570f921053441fb3c14d1274d8a827049 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/f1b140f84d26166d4fa75eb072276a3a118f092d...5dbd0ce570f921053441fb3c14d1274d8a827049 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
