[med-svn] [Git][med-team/ncbi-igblast][master] 4 commits: avoid-gcc-crash.patch (new): Work around a consistent ICE

[Aaron M. Ucko (@ucko)]

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 <tille at debian.org>  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 <ucko at debian.org>  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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230120/7e062950/attachment-0001.htm>