[med-svn] [Git][med-team/ncbi-blastplus][master] 8 commits: override_dh_clean: rm -rf fakehome c++/include/common/ncbi_revision.h
Aaron M. Ucko
gitlab at salsa.debian.org
Mon Apr 27 00:42:40 BST 2020
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus
Commits:
bdbae23d by Aaron M. Ucko at 2020-04-26T17:51:01-04:00
override_dh_clean: rm -rf fakehome c++/include/common/ncbi_revision.h
- - - - -
c3e321f1 by Aaron M. Ucko at 2020-04-26T17:58:16-04:00
+ d/patches/support_gcc10 for formal support of GCC 10+ (#957581).
- - - - -
3c25a8bc by Aaron M. Ucko at 2020-04-26T19:30:04-04:00
override_dh_install-arch: No .py for new cleanup-blastdb-volumes.
- - - - -
75d69f12 by Aaron M. Ucko at 2020-04-26T19:30:51-04:00
+ d/patches/run_perl_directly for update_blastdb(.pl)'s #! line.
- - - - -
501c028c by Aaron M. Ucko at 2020-04-26T19:30:51-04:00
debian/rules: Half clean up -Wl,-as-needed.
Stop directly injecting -Wl,--as-needed into LDFLAGS, but keep
DEB_LDFLAGS_MAINT_APPEND for the sake of backports, along with a
comment that they can't rely on GCC 9+.
- - - - -
36632f0f by Aaron M. Ucko at 2020-04-26T19:32:56-04:00
routine-update: Add salsa-ci file
- - - - -
77b9f02e by Aaron M. Ucko at 2020-04-26T19:35:09-04:00
Wrap long lines in changelog entries: 2.2.25-6.
Fixes: lintian: debian-changelog-line-too-long
See-also: https://lintian.debian.org/tags/debian-changelog-line-too-long.html
- - - - -
ea0764c2 by Aaron M. Ucko at 2020-04-26T19:38:14-04:00
Finalize ncbi-blast+ 2.10.0-1 for unstable.
- - - - -
6 changed files:
- debian/changelog
- + debian/patches/run_perl_directly
- debian/patches/series
- + debian/patches/support_gcc10
- debian/rules
- + debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,23 @@
-ncbi-blast+ (2.10.0-1) UNRELEASED; urgency=medium
+ncbi-blast+ (2.10.0-1) unstable; urgency=medium
- * New upstream release. (NOT RELEASED YET.)
- * debian/patches: Formally refresh. (A few files needed straightforward
- manual intervention.)
-
- -- Aaron M. Ucko <ucko at debian.org> Sat, 25 Apr 2020 22:13:31 -0400
+ * New upstream release.
+ * debian/patches:
+ - Formally refresh. (A few files needed straightforward manual
+ intervention.)
+ - support_gcc10: New, for formal support of GCC 10+. (Closes: #957581.)
+ - run_perl_directly: New, to streamline update_blastdb(.pl)'s #! line.
+ * debian/rules:
+ - override_dh_clean: Clean up new generated artifacts: fakehome/ and
+ c++/include/common/ncbi_revision.h.
+ - override_dh_install-arch: Install new cleanup-blastdb-volumes script
+ without its upstream .py suffix.
+ - Stop directly injecting -Wl,--as-needed into LDFLAGS, but keep
+ DEB_LDFLAGS_MAINT_APPEND for the sake of backports, along with a
+ comment that they can't rely on GCC 9+.
+ * Add salsa-ci file (routine-update)
+ * Wrap long lines in changelog entries: 2.2.25-6.
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 26 Apr 2020 19:38:13 -0400
ncbi-blast+ (2.9.0-4) unstable; urgency=high
@@ -383,7 +396,8 @@ ncbi-blast+ (2.2.25-7) unstable; urgency=low
ncbi-blast+ (2.2.25-6) unstable; urgency=low
* debian/control:
- Luca Capello <luca at pca.it>, fix reference for legacy_blast (Closes: #642986).
+ + Luca Capello <luca at pca.it>, fix reference for legacy_blast
+ (Closes: #642986).
+ add a new line to separate the actual description from usage
instruction in the long Description:.
* debian/rules: add gene_info_reader binary in package
=====================================
debian/patches/run_perl_directly
=====================================
@@ -0,0 +1,12 @@
+Author: Aaron M. Ucko <ucko at debian.org>
+Date: Sun Apr 26 11:28:03 2020 -0400
+Description: Bypass env in Perl script shebangs.
+
+--- a/c++/src/app/blast/update_blastdb.pl
++++ b/c++/src/app/blast/update_blastdb.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ # $Id: update_blastdb.pl 597648 2019-11-25 18:31:12Z ivanov $
+ # ===========================================================================
+ #
=====================================
debian/patches/series
=====================================
@@ -13,3 +13,5 @@ fix_unit_tests
system_mbedtls_only
reprobuild
spelling
+support_gcc10
+run_perl_directly
=====================================
debian/patches/support_gcc10
=====================================
@@ -0,0 +1,388 @@
+Author: Aaron M. Ucko <ucko at debian.org>
+Date: Sun Apr 26 11:20:45 2020 -0400
+Description: Support GCC 10+.
+Debian-Bug: 957581.
+
+Formally recognize GCC 10 and up, even if (as in Debian) -dumpversion
+reports only one or two components of the version number. Corresponds to
+
+https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88985
+https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88988
+https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=88989
+https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=89711
+
+though the last of those doesn't apply cleanly without some
+intervening changes for better Clang support.
+
+--- a/c++/src/build-system/config.h.in
++++ b/c++/src/build-system/config.h.in
+@@ -966,7 +966,7 @@
+ /* Compiler name */
+ #undef NCBI_COMPILER_UNKNOWN
+
+-/* Compiler version as three-digit integer */
++/* Compiler version as three- or four-digit integer */
+ #undef NCBI_COMPILER_VERSION
+
+ /* Compiler name */
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -8233,9 +8233,10 @@ fi
+ case "$compiler:$ncbi_compiler_ver" in
+ WorkShop*:?.?? ) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\)/\1\20/' ;;
+ WorkShop*:[6-9].?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9\)/\10\20/' ;;
+- ICC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;
+- ICC:??.?.? | \
+- ICC:??.?.?.* ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;
++ [GI]CC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;
++ GCC:??.?.? | ICC:??.?.? | ICC:??.?.?.* )
++ ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;
++ GCC:?? ) ncbi_compiler_sed='s/\([0-9][0-9]\)/\100/' ;;
+ *:?.?.?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9]\)\.\([0-9]\)/\1\2\3/' ;;
+ *:?.??*) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\).*/\1\2/' ;;
+ *:?.?) ncbi_compiler_sed='s/\([0-9]\).\([0-9]\)/\1\20/' ;;
+@@ -8455,10 +8456,7 @@ if test "$with_mt" != "no" ; then
+ # Will allegedly support -openmp at some point, but as of 3.4,
+ # just parses it as specifying an output filename: -o penmp.
+ else
+- case "$compiler_version" in
+- [123]?? | 4[01]? ) ;;
+- * ) : ${OPENMP_FLAGS=-fopenmp} ;;
+- esac
++ : ${OPENMP_FLAGS=-fopenmp}
+ fi
+ ;;
+ ICC )
+@@ -8510,16 +8508,14 @@ case "$host_os:$compiler" in
+ # "incomplete type is not allowed" should be an error, not a warning!
+ CFLAGS="-we70 $CFLAGS"
+ CXXFLAGS="-we70 $CXXFLAGS"
+- case "$compiler_version" in
+- 1[1-9]?? ) MATH_LIBS=-Wl,-lm ;; # avoid static libimf in shared libs
+- esac
++ MATH_LIBS=-Wl,-lm # avoid static libimf in shared libs
+ ;;
+
+ linux*:GCC )
+ if test -r $srcdir/src/build-system/config.site.ncbi && test -d "$NCBI"
+ then
+ case "$compiler_version" in
+- 5* ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;
++ 5?? ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;
+ esac
+ fi
+ ;;
+@@ -9888,7 +9884,7 @@ esac
+ ### large file support (switch to AC_SYS_LARGEFILE?)
+ case "$host_os:$compiler:$compiler_version" in
+ cygwin* ) with_lfs=no ;;
+- *:GCC:3[4-9]* | *:GCC:[4-9]* | *:ICC:[91]* ) : ${with_lfs=yes} ;;
++ *:GCC:* | *:ICC:* ) : ${with_lfs=yes} ;;
+ esac
+
+ if test "$with_lfs" = "yes" ; then
+@@ -9910,17 +9906,9 @@ wsrx="[$wschars]"
+ #### Flags to enable (potentially unsafe) extra optimization.
+ if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
+ case "$compiler:$compiler_version" in
+- GCC:2* | GCC:344 )
+- # GCC 2.9x sometimes experiences internal errors at high optimization;
+- # GCC 3.4.4 (at least on FreeBSD) meanwhile generates crashprone code.
+- DEF_FAST_FLAGS="-O2"
+- ;;
+ GCC:* )
+ DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"
+- case "$host_os:$host_cpu:$compiler_version" in
+- freebsd* | solaris*:*86*:* | *:4[5-9]? | *:[5-9]?? ) ;;
+- * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
+- esac
++ # DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
+ if test "$with_profiling" != "yes"; then
+ # incompatible with -pg
+ DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer"
+@@ -9958,15 +9946,6 @@ if test "$skip_fast_flags" = no -a -z "$
+ solaris* ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fast $ARCH_CFLAGS" ;;
+ esac
+ ;;
+- ICC:[1-8]?? )
+- DEF_FAST_FLAGS="-O2"
+- ;;
+- ICC:9?? )
+- DEF_FAST_FLAGS="-O3 -axP -ip" # optimized for Core or P4 w/SSE3 (max)
+- ;;
+- ICC:10?? )
+- DEF_FAST_FLAGS="-O3 -axT -ip" # Core 2 w/SSSE3; axS would cover SSE 4.1
+- ;;
+ ICC:* )
+ # Core 2; ICC 11 goes up to SSE4.2 (i7), ICC 12 up to CORE-AVX-I
+ DEF_FAST_FLAGS="-O3 -axSSSE3 -ip"
+@@ -10108,12 +10087,7 @@ echo "$as_me: error: Unable to find stat
+ ;;
+ GCC:* )
+ # Need to specify runpath for compiler-provided libraries
+- case $compiler_version in
+- 30* ) major=3 ;;
+- 31* ) major=4 ;;
+- 3[23]*) major=5 ;;
+- * ) major=6 ;;
+- esac
++ major=6 # true for all supported versions at present
+ found=false
+ for f in libstdc++.so.$major libgcc_s.so.1 libstdc++.a; do
+ path=`$CXX $LDFLAGS -print-file-name=$f`
+@@ -10294,9 +10268,6 @@ esac
+ if test "$compiler" = "GCC" ; then
+ CFLAGS="-Wall -Wno-format-y2k $CFLAGS"
+ CXXFLAGS="-Wall -Wno-format-y2k $CXXFLAGS"
+- case "$compiler_version" in
+- 2* ) CXXFLAGS="-ftemplate-depth-32 $CXXFLAGS" ;;
+- esac
+ case "$host_os" in
+ solaris* ) CPPFLAGS="-D__EXTENSIONS__ $CPPFLAGS" ;;
+ irix* ) CXXFLAGS="$CXXFLAGS -D_LANGUAGE_C_PLUS_PLUS" ;;
+@@ -13214,13 +13185,11 @@ _ACEOF
+ ;;
+ linux* | *gnu* ) # | *bsd*
+ case "$compiler:$compiler_version" in
+- ICC:9* | ICC:1??? )
++ ICC:* )
+ ncbi_cv_prog_cc_wl_no_asu=no
+ LIBS="$LIBS -lc"
+ C_LIBS="$C_LIBS -lc"
+ ;;
+- ICC:* )
+- ;;
+ * )
+ FORBID_UNDEF='-Wl,--no-undefined'
+ ;;
+@@ -13963,7 +13932,7 @@ echo "$as_me: error: --with-max-debug=$w
+ echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"
+ STRIP="@:"
+ case "$compiler:$compiler_version" in
+- GCC:4[89]? | GCC:[5-9]? | GCC:???? )
++ GCC:* )
+ # GCC 4.8 defaults to DWARF 4, which Totalview for one
+ # can't handle; roll back to version 3 by default.
+ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
+@@ -25344,10 +25313,6 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+ # Avoid using unsupported (and noisily ignored) attributes.
+ case "$compiler:$compiler_version" in
+- GCC:2* | GCC:3[01]* )
+- ncbi_cv_c_deprecation_syntax=none
+- ncbi_cv_c_forceinline=inline
+- ;;
+ VisualAge:* )
+ ncbi_cv_c_forceinline=inline
+ ;;
+@@ -25585,7 +25550,7 @@ _ACEOF
+ fi
+
+ case "$compiler:$compiler_version $CFLAGS $CXXFLAGS" in
+- GCC:[4-9]??\ *\ -fvisibility*|ICC:*\ -fvisibility* ) ;;
++ GCC:*\ *\ -fvisibility* | ICC:*\ -fvisibility* ) ;;
+ * ) ncbi_cv_c_attribute_visibility_default=unnecessary ;;
+ esac
+
+@@ -37178,7 +37143,7 @@ _ACEOF
+ # when using Boost at all.
+ BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"
+ ;;
+- GCC*:4[7-9]* | GCC*:5*)
++ GCC*)
+ # Some portions of Boost also have a lot of "unused" typedefs
+ # from concept checking.
+ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"
+@@ -37221,6 +37186,7 @@ echo $ECHO_N "checking for Boost library
+ *:MSVC) BOOST_TAG="-vc" ;;
+ esac
+ case "$BOOST_TAG" in
++ # Still valid for version 10.x and up?
+ -*gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;
+ * ) boost_comp_vers='' ;;
+ esac
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1257,9 +1257,10 @@ changequote(, )dnl
+ case "$compiler:$ncbi_compiler_ver" in
+ WorkShop*:?.?? ) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\)/\1\20/' ;;
+ WorkShop*:[6-9].?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9\)/\10\20/' ;;
+- ICC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;
+- ICC:??.?.? | \
+- ICC:??.?.?.* ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;
++ [GI]CC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;;
++ GCC:??.?.? | ICC:??.?.? | ICC:??.?.?.* )
++ ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;
++ GCC:?? ) ncbi_compiler_sed='s/\([0-9][0-9]\)/\100/' ;;
+ *:?.?.?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9]\)\.\([0-9]\)/\1\2\3/' ;;
+ *:?.??*) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\).*/\1\2/' ;;
+ *:?.?) ncbi_compiler_sed='s/\([0-9]\).\([0-9]\)/\1\20/' ;;
+@@ -1287,7 +1288,7 @@ fi
+ AC_DEFINE_UNQUOTED(NCBI_COMPILER, "$ncbi_compiler", [Compiler name])
+ AC_DEFINE_UNQUOTED(NCBI_COMPILER_$ncbi_compiler, 1, [Compiler name])
+ AC_DEFINE_UNQUOTED(NCBI_COMPILER_VERSION, $ncbi_compiler_ver,
+- [Compiler version as three-digit integer])
++ [Compiler version as three- or four-digit integer])
+
+
+ #### Additional check for pre-defined compilers
+@@ -1407,10 +1408,7 @@ if test "$with_mt" != "no" ; then
+ # Will allegedly support -openmp at some point, but as of 3.4,
+ # just parses it as specifying an output filename: -o penmp.
+ else
+- case "$compiler_version" in
+- [[123]]?? | 4[[01]]? ) ;;
+- * ) : ${OPENMP_FLAGS=-fopenmp} ;;
+- esac
++ : ${OPENMP_FLAGS=-fopenmp}
+ fi
+ ;;
+ ICC )
+@@ -1462,16 +1460,14 @@ case "$host_os:$compiler" in
+ # "incomplete type is not allowed" should be an error, not a warning!
+ CFLAGS="-we70 $CFLAGS"
+ CXXFLAGS="-we70 $CXXFLAGS"
+- case "$compiler_version" in
+- 1[[1-9]]?? ) MATH_LIBS=-Wl,-lm ;; # avoid static libimf in shared libs
+- esac
++ MATH_LIBS=-Wl,-lm # avoid static libimf in shared libs
+ ;;
+
+ linux*:GCC )
+ if test -r $srcdir/src/build-system/config.site.ncbi && test -d "$NCBI"
+ then
+ case "$compiler_version" in
+- 5* ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;
++ 5?? ) CPPFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0 $CPPFLAGS" ;;
+ esac
+ fi
+ ;;
+@@ -2046,7 +2042,7 @@ esac
+ ### large file support (switch to AC_SYS_LARGEFILE?)
+ case "$host_os:$compiler:$compiler_version" in
+ cygwin* ) with_lfs=no ;;
+- *:GCC:3[[4-9]]* | *:GCC:[[4-9]]* | *:ICC:[[91]]* ) : ${with_lfs=yes} ;;
++ *:GCC:* | *:ICC:* ) : ${with_lfs=yes} ;;
+ esac
+
+ if test "$with_lfs" = "yes" ; then
+@@ -2068,17 +2064,9 @@ wsrx="[[$wschars]]"
+ #### Flags to enable (potentially unsafe) extra optimization.
+ if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then
+ case "$compiler:$compiler_version" in
+- GCC:2* | GCC:344 )
+- # GCC 2.9x sometimes experiences internal errors at high optimization;
+- # GCC 3.4.4 (at least on FreeBSD) meanwhile generates crashprone code.
+- DEF_FAST_FLAGS="-O2"
+- ;;
+ GCC:* )
+ DEF_FAST_FLAGS="-O3 -finline-functions -fstrict-aliasing"
+- case "$host_os:$host_cpu:$compiler_version" in
+- freebsd* | solaris*:*86*:* | *:4[[5-9]]? | *:[[5-9]]?? ) ;;
+- * ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
+- esac
++ # DEF_FAST_FLAGS="$DEF_FAST_FLAGS -ffast-math" ;;
+ if test "$with_profiling" != "yes"; then
+ # incompatible with -pg
+ DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fomit-frame-pointer"
+@@ -2116,15 +2104,6 @@ if test "$skip_fast_flags" = no -a -z "$
+ solaris* ) DEF_FAST_FLAGS="$DEF_FAST_FLAGS -fast $ARCH_CFLAGS" ;;
+ esac
+ ;;
+- ICC:[[1-8]]?? )
+- DEF_FAST_FLAGS="-O2"
+- ;;
+- ICC:9?? )
+- DEF_FAST_FLAGS="-O3 -axP -ip" # optimized for Core or P4 w/SSE3 (max)
+- ;;
+- ICC:10?? )
+- DEF_FAST_FLAGS="-O3 -axT -ip" # Core 2 w/SSSE3; axS would cover SSE 4.1
+- ;;
+ ICC:* )
+ # Core 2; ICC 11 goes up to SSE4.2 (i7), ICC 12 up to CORE-AVX-I
+ DEF_FAST_FLAGS="-O3 -axSSSE3 -ip"
+@@ -2225,12 +2204,7 @@ case "$compiler:$compiler_version:$with_
+ ;;
+ GCC:* )
+ # Need to specify runpath for compiler-provided libraries
+- case $compiler_version in
+- 30* ) major=3 ;;
+- 31* ) major=4 ;;
+- 3[[23]]*) major=5 ;;
+- * ) major=6 ;;
+- esac
++ major=6 # true for all supported versions at present
+ found=false
+ for f in libstdc++.so.$major libgcc_s.so.1 libstdc++.a; do
+ path=`$CXX $LDFLAGS -print-file-name=$f`
+@@ -2388,9 +2362,6 @@ AC_SUBST(USUAL_AND_LIB)
+ if test "$compiler" = "GCC" ; then
+ CFLAGS="-Wall -Wno-format-y2k $CFLAGS"
+ CXXFLAGS="-Wall -Wno-format-y2k $CXXFLAGS"
+- case "$compiler_version" in
+- 2* ) CXXFLAGS="-ftemplate-depth-32 $CXXFLAGS" ;;
+- esac
+ case "$host_os" in
+ solaris* ) CPPFLAGS="-D__EXTENSIONS__ $CPPFLAGS" ;;
+ irix* ) CXXFLAGS="$CXXFLAGS -D_LANGUAGE_C_PLUS_PLUS" ;;
+@@ -3029,13 +3000,11 @@ case "$compiler" in
+ ;;
+ linux* | *gnu* ) # | *bsd*
+ case "$compiler:$compiler_version" in
+- ICC:9* | ICC:1??? )
++ ICC:* )
+ ncbi_cv_prog_cc_wl_no_asu=no
+ LIBS="$LIBS -lc"
+ C_LIBS="$C_LIBS -lc"
+ ;;
+- ICC:* )
+- ;;
+ * )
+ FORBID_UNDEF='-Wl,--no-undefined'
+ ;;
+@@ -3319,7 +3288,7 @@ changequote(, )dnl
+ echo " $LDFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || LDFLAGS="$LDFLAGS -g"
+ STRIP="@:"
+ case "$compiler:$compiler_version" in
+- GCC:4[89]? | GCC:[5-9]? | GCC:???? )
++ GCC:* )
+ # GCC 4.8 defaults to DWARF 4, which Totalview for one
+ # can't handle; roll back to version 3 by default.
+ echo " $USER_CFLAGS " | $EGREP_Q "$dbgrx1|$dbgrx2" || \
+@@ -3929,10 +3898,6 @@ AC_LANG_POP(C)
+
+ # Avoid using unsupported (and noisily ignored) attributes.
+ case "$compiler:$compiler_version" in
+- GCC:2* | GCC:3[[01]]* )
+- ncbi_cv_c_deprecation_syntax=none
+- ncbi_cv_c_forceinline=inline
+- ;;
+ VisualAge:* )
+ ncbi_cv_c_forceinline=inline
+ ;;
+@@ -3985,7 +3950,7 @@ if test $ncbi_cv_c_attribute_destructor
+ fi
+
+ case "$compiler:$compiler_version $CFLAGS $CXXFLAGS" in
+- GCC:[[4-9]]??\ *\ -fvisibility*|ICC:*\ -fvisibility* ) ;;
++ GCC:*\ *\ -fvisibility* | ICC:*\ -fvisibility* ) ;;
+ * ) ncbi_cv_c_attribute_visibility_default=unnecessary ;;
+ esac
+
+@@ -5632,7 +5597,7 @@ ncbi_cv_lib_boost_version=\`get_BOOST_LI
+ # when using Boost at all.
+ BOOST_INCLUDE="$BOOST_INCLUDE -erroff=reftotemp"
+ ;;
+- GCC*:4[[7-9]]* | GCC*:5*)
++ GCC*)
+ # Some portions of Boost also have a lot of "unused" typedefs
+ # from concept checking.
+ BOOST_INCLUDE="$BOOST_INCLUDE -Wno-unused-local-typedefs"
+@@ -5672,6 +5637,7 @@ ncbi_cv_lib_boost_version=\`get_BOOST_LI
+ *:MSVC) BOOST_TAG="-vc" ;;
+ esac
+ case "$BOOST_TAG" in
++ # Still valid for version 10.x and up?
+ -*gcc|-il ) boost_comp_vers=`echo $compiler_version | cut -c1-2` ;;
+ * ) boost_comp_vers='' ;;
+ esac
=====================================
debian/rules
=====================================
@@ -26,13 +26,12 @@ DEB_CONFIGURE_EXTRA_FLAGS += --with-symbols
#export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic
+# Kept for the sake of backports, which can't rely on GCC 9+.
export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed
include /usr/share/dpkg/architecture.mk
include /usr/share/dpkg/buildflags.mk
-LDFLAGS += -Wl,--as-needed
-
ifneq (,$(findstring mips,$(DEB_HOST_ARCH)))
CXXFLAGS := $(CXXFLAGS:-O%=-O)
DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O
@@ -99,6 +98,8 @@ override_dh_install-arch:
mv $(instroot)/bin/seedtop $(instroot)/bin/seedtop+
mv $(instroot)/bin/get_species_taxids.sh \
$(instroot)/bin/get_species_taxids
+ mv $(instroot)/bin/cleanup-blastdb-volumes.py \
+ $(instroot)/bin/cleanup-blastdb-volumes
mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast
mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb
sed -e '1s/$$/3/' $(instroot)/bin/windowmasker_2.2.22_adapter.py \
@@ -157,8 +158,9 @@ override_dh_clean:
done
rm -rf c++/compilers/dll c++/config.log c++/Makefile
rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module
+ rm -f c++/include/common/ncbi_revision.h
find -name check_exec.pid -delete
- rm -rf c++/BUILD c++/BUILD.native
+ rm -rf c++/BUILD c++/BUILD.native fakehome
mv configure.orig.save c++/configure.orig
mv c++/src/util/lmdb/Makefile.orig.save c++/src/util/lmdb/Makefile.orig
mv c++/src/util/lmdbxx/Makefile.orig.save c++/src/util/lmdbxx/Makefile.orig
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/ef898b4071b9b52c91692c9a434937c1c73041ca...ea0764c2e03c42daa0fc5fc7e78d5c31256f6b6f
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