[med-svn] [Git][med-team/arb][master] 10 commits: Drop patches applied upstream in 7.0
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 23 08:43:55 BST 2026
Andreas Tille pushed to branch master at Debian Med / arb
Commits:
0e5410fd by Andreas Tille at 2026-10-23T09:35:40+02:00
Drop patches applied upstream in 7.0
Patches 10, 20, 30 and 40 are part of upstream 7.0 and no longer apply.
- - - - -
c5067c7f by Andreas Tille at 2026-10-23T09:35:50+02:00
Refresh phyml and MAFFT patches for upstream 7.0
Adapt the patch context to the updated upstream makefiles.
- - - - -
b87836b8 by Andreas Tille at 2026-10-23T09:35:58+02:00
Refresh compiler and linker patches for upstream 7.0
Update the context of the compiler-version-check and RPATH patches and re-apply the tirpc flags at their new locations.
Also allow C++ standards newer than C++14 in cxxforward.h, needed for the no-standard compatibility build with GCC 16.
- - - - -
415e040f by Andreas Tille at 2026-10-23T09:36:05+02:00
Refresh gcc-16 patch for upstream 7.0
Keep only the PROBE/PT_new_design.cxx const fix; the CAP2.c source no longer exists upstream.
- - - - -
47702207 by Andreas Tille at 2026-10-23T09:36:26+02:00
Add new build dependencies for upstream 7.0
Upstream now uses Boost.Random in ARBDB and Xerces-C in PROBE_DESIGN.
- - - - -
9743015c by Andreas Tille at 2026-10-23T09:37:31+02:00
Disable vectorization checks under GCC 16
GCC 16 fails some LOOP_VECTORIZED checks, e.g. in CORE/arb_strarray.cxx, causing a FTBFS. Vectorization itself is unaffected; only the compile-time verification is disabled.
- - - - -
4d20f00f by Andreas Tille at 2026-10-23T09:37:51+02:00
Build bundled RAxML/SATIVA sources as C17
GCC 16 defaults to C23, where 'bool' is a keyword and the old bundled RAxML and SATIVA sources no longer compile. Build them as C17 with -fcommon to retain their common symbols.
- - - - -
22b32218 by Andreas Tille at 2026-10-23T09:38:11+02:00
Build C sources as C17 under GCC 16
GCC 16 defaults to C23, which breaks old ARB C sources such as GDE/SUPPORT/count.c. Build them as C17 and strip that option again for the no-standard C++ compatibility target.
- - - - -
1667d43f by Andreas Tille at 2026-10-23T09:38:25+02:00
Use dh_missing for debhelper compat 14
dh_install --list-missing was removed in compat 12. Call dh_install and override dh_missing with --list-missing to keep the previous, non-fatal behaviour.
- - - - -
488efa9f by Andreas Tille at 2026-10-23T09:38:36+02:00
Update changelog for the 7.0 packaging fixes
- - - - -
17 changed files:
- debian/changelog
- debian/control
- debian/patches/100_use_tirpc.patch
- − debian/patches/10_upstream_r12793__show_db_load_progress
- + debian/patches/120_disable_vectorize_check.patch
- + debian/patches/130_bundled_raxml_build_c17.patch
- + debian/patches/140_compile_compat_strip_c_std.patch
- − debian/patches/20_upstream_r12794__socket_permissions
- − debian/patches/30_upstream_r12814__desktop_keywords
- − debian/patches/40_upstream_r12815__lintian_spelling
- debian/patches/60_use_packaged_phyml
- debian/patches/70_skip_compler_version_check.patch
- debian/patches/80_enable_new_dtags.patch
- debian/patches/90_do_not_create_MAFFT_symlinks.patch
- debian/patches/gcc-16+
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -15,6 +15,14 @@ arb (7.0-1) UNRELEASED; urgency=medium
* New upstream version
* Reformat the Last-Update date as ISO YYYY-MM-DD.
* debputy lint --auto-fix (routine-update)
+ * Adapt patches to the new upstream version:
+ - Drop 10, 20, 30 and 40, which were applied upstream.
+ - Refresh the remaining patches for the new source layout.
+ - Add 120 to disable GCC 16 vectorization checks.
+ - Add 130 to build bundled RAxML/SATIVA sources as C17.
+ - Add 140 to strip the C standard from the 'nostd' compatibility build.
+ * Add libboost-dev and libxerces-c-dev to Build-Depends.
+ * d/rules: build C sources as C17 and use dh_missing for compat 14.
-- Andreas Tille <tille at debian.org> Fri, 23 Oct 2026 07:24:51 +0200
=====================================
debian/control
=====================================
@@ -12,6 +12,7 @@ Build-Depends:
freeglut3-dev | libglu-dev,
libb-lint-perl,
libbio-perl-perl,
+ libboost-dev,
libglew-dev,
libglib2.0-dev,
libglu1-mesa-dev,
@@ -21,6 +22,7 @@ Build-Depends:
libtiff-dev,
libtirpc-dev,
libxaw7-dev,
+ libxerces-c-dev,
libxml2-utils,
libxpm-dev,
lynx,
=====================================
debian/patches/100_use_tirpc.patch
=====================================
@@ -1,37 +1,38 @@
Description: Append relevant flags to cxxflags and lfags to build with tirpc
+ Also accept C++ standards newer than C++14 in cxxforward.h. GCC 16 uses
+ C++23 by default for the no-standard compatibility build.
Author: Nilesh Patra <nilesh at debian.org>
-Last-Update: 2021-11-06
+Last-Update: 2026-10-23
+Assisted-By: deepseek-v4.1-flash-free
+
--- a/Makefile
+++ b/Makefile
-@@ -523,7 +523,7 @@
+@@ -873,7 +873,7 @@
# add CFLAGS + CPPFLAGS from environment for DEBIAN build
ifeq ($(DEBIAN),1)
- cflags := $(CFLAGS) $(cflags)
-- cxxflags += $(CPPFLAGS)
-+ cxxflags += $(CPPFLAGS) -I/usr/include/tirpc
+ cflags := $(CFLAGS) $(cflags)
+- cxxflags += $(CPPFLAGS)
++ cxxflags += $(CPPFLAGS) -I/usr/include/tirpc
endif
- ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
-@@ -563,7 +563,7 @@
- # make -j9 "TIMED_TARGET=perl" clean_timed_target | grep '^\[' | sort
+ ifeq ('$(USE_CLANG)','1')
+@@ -935,7 +935,7 @@
+ # Note: definitions exported to sub-makefiles are described in SOURCE_TOOLS/parent_make.txt
CORE_LIB=-lCORE
-ARBDB_LIB=-lARBDB $(CORE_LIB)
+ARBDB_LIB=-lARBDB $(CORE_LIB) -ltirpc
- LIBS = $(ARBDB_LIB) $(SYSLIBS)
+ DBSYS_LIBS = $(ARBDB_LIB) $(SYSLIBS)
GUI_LIBS_PREFIX:=
--- a/TEMPLATES/cxxforward.h
+++ b/TEMPLATES/cxxforward.h
-@@ -28,7 +28,11 @@
- # define ARB_ENABLE_Cxx11_FEATURES
- // # define ARB_ENABLE_Cxx14_FEATURES // not needed yet
+@@ -23,7 +23,7 @@
+ # if (__cplusplus == 201103L)
+ # define ARB_ENABLE11_FEATURES
+ # else
+-# if (__cplusplus == 201402L)
++# if (__cplusplus >= 201402L)
+ # define ARB_ENABLE11_FEATURES
+ # define ARB_ENABLE14_FEATURES
# else
-+# if (__cplusplus == 201703L)
-+# define ARB_ENABLE_Cxx11_FEATURES
-+# else
- # error Unknown C++ standard defined in __cplusplus
-+# endif
- # endif
- # endif
- # endif
=====================================
debian/patches/10_upstream_r12793__show_db_load_progress deleted
=====================================
@@ -1,138 +0,0 @@
-Author: Elmar Pruesse <elmar at pruesse.net>
-Last-Update: 2014-09-02
-Description:show progress while ARB is loading a database
- (needed as indicator/splash screen while ARB is launching)
-Origin: upstream, http://bugs.arb-home.de/log/trunk?revs=12792-12793,12795
-
---- a/ARBDB/ad_load.cxx
-+++ b/ARBDB/ad_load.cxx
-@@ -17,6 +17,7 @@
- #include <arb_str.h>
- #include <arb_file.h>
- #include <arb_defs.h>
-+#include <arb_progress.h>
-
- #include "gb_key.h"
- #include "gb_localdata.h"
-@@ -655,12 +656,18 @@ static void DEBUG_DUMP_INDENTED(long dee
- #endif // DEBUG_READ
- // ----------------------------------------
-
--
--static long gb_read_bin_rek_V2(FILE *in, GBCONTAINER *gbc_dest, long nitems, long version, long reversed, long deep) {
-+static long gb_read_bin_rek_V2(FILE *in, GBCONTAINER *gbc_dest, long nitems, long version,
-+ long reversed, long deep, arb_progress& progress) {
- GB_MAIN_TYPE *Main = GB_MAIN(gbc_dest);
-
- DEBUG_DUMP_INDENTED(deep, GBS_global_string("Reading container with %li items", nitems));
-
-+ progress.inc_to(ftell(in));
-+ if (progress.aborted()) {
-+ GB_export_error(progress.error_if_aborted());
-+ return -1;
-+ }
-+
- gb_create_header_array(gbc_dest, (int)nitems);
- gb_header_list *header = GB_DATA_LIST_HEADER(gbc_dest->d);
- if (deep == 0 && GBCONTAINER_MAIN(gbc_dest)->allow_corrupt_file_recovery) {
-@@ -849,7 +856,7 @@ static long gb_read_bin_rek_V2(FILE *in,
- case GB_DB: {
- long size = gb_get_number(in);
- // gbc->d.size is automatically incremented
-- if (gb_read_bin_rek_V2(in, gbc, size, version, reversed, deep+1)) {
-+ if (gb_read_bin_rek_V2(in, gbc, size, version, reversed, deep+1, progress)) {
- if (!GBCONTAINER_MAIN(gbc_dest)->allow_corrupt_file_recovery) {
- return -1;
- }
-@@ -922,7 +929,7 @@ inline bool read_keyword(const char *exp
- return as_expected;
- }
-
--static long gb_read_bin(FILE *in, GBCONTAINER *gbc, bool allowed_to_load_diff) {
-+static long gb_read_bin(FILE *in, GBCONTAINER *gbc, bool allowed_to_load_diff, arb_progress& progress) {
- int c = 1;
- long i;
- long error;
-@@ -1153,7 +1160,7 @@ static long gb_read_bin(FILE *in, GBCONT
- if (Main->clock<=0) Main->clock++;
- // fall-through
- case 1: // master arb file
-- error = gb_read_bin_rek_V2(in, gbc, nodecnt, version, reversed, 0);
-+ error = gb_read_bin_rek_V2(in, gbc, nodecnt, version, reversed, 0, progress);
- break;
- default:
- GB_internal_errorf("Sorry: This ARB Version does not support database format V%li", version);
-@@ -1445,7 +1452,10 @@ static GBDATA *GB_login(const char *cpat
- i = (input != stdin) ? gb_read_in_uint32(input, 0) : 0;
-
- if (is_binary_db_id(i)) {
-- i = gb_read_bin(input, gbc, false); // read or map whole db
-+ {
-+ arb_progress progress("Loading database", GB_size_of_FILE(input));
-+ i = gb_read_bin(input, gbc, false, progress); // read or map whole db
-+ }
- gbc = Main->root_container;
- fclose(input);
-
-@@ -1486,7 +1496,10 @@ static GBDATA *GB_login(const char *cpat
- }
- i = gb_read_in_uint32(input, 0);
- if (is_binary_db_id(i)) {
-- err = gb_read_bin(input, gbc, true);
-+ {
-+ arb_progress progress("Loading quicksave", GB_size_of_FILE(input) / 1024);
-+ err = gb_read_bin(input, gbc, true, progress);
-+ }
- fclose (input);
-
- if (err) {
---- a/CORE/arb_progress.cxx
-+++ b/CORE/arb_progress.cxx
-@@ -22,6 +22,7 @@ struct null_counter: public arb_progress
-
- void inc() OVERRIDE {}
- void implicit_inc() OVERRIDE {}
-+ void inc_to(int x) OVERRIDE {}
- void done() OVERRIDE {}
- void restart(int) OVERRIDE {}
- void force_update() OVERRIDE {}
-@@ -142,6 +143,13 @@ public:
-
- void inc() OVERRIDE { explicit_counter += 1; update_display_if_needed(); }
- void implicit_inc() OVERRIDE { implicit_counter += 1; update_display_if_needed(); }
-+ void inc_to(int x) {
-+ explicit_counter = std::max(explicit_counter, x);
-+ if (maxcount) {
-+ explicit_counter = std::min(explicit_counter, maxcount);
-+ }
-+ update_display_if_needed();
-+ }
-
- void done() OVERRIDE {
- implicit_counter = explicit_counter = maxcount;
---- a/CORE/arb_progress.h
-+++ b/CORE/arb_progress.h
-@@ -44,6 +44,7 @@ public:
-
- virtual void inc() = 0;
- virtual void implicit_inc() = 0;
-+ virtual void inc_to(int x) = 0;
- virtual void child_updates_gauge(double gauge) = 0;
- virtual void done() = 0;
- virtual void force_update() = 0;
-@@ -131,6 +132,7 @@ public:
- void force_update() { counter->force_update(); }
-
- void inc() { counter->inc(); }
-+ void inc_to(int x) { counter->inc_to(x); }
- void done() { counter->done(); }
- void auto_subtitles(const char *prefix) { counter->auto_subtitles(prefix); }
-
-@@ -244,6 +246,7 @@ public:
- const arb_progress& operator++() { inc(); return *this; } // ++progress
-
- void inc_by(int count) { arb_assert(count>0); while (count--) inc(); }
-+ void inc_to(int x) { used->inc_to(x); }
-
- void sub_progress_skipped() { used->child_terminated(); }
-
=====================================
debian/patches/120_disable_vectorize_check.patch
=====================================
@@ -0,0 +1,18 @@
+Description: Disable vectorization checks for Debian builds
+ GCC 16 fails some LOOP_VECTORIZED checks (e.g. in CORE/arb_strarray.cxx),
+ which causes a FTBFS. The vectorization itself is unaffected; only the
+ compile-time verification is turned off.
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-10-23
+Assisted-By: deepseek-v4.1-flash-free
+
+--- a/Makefile
++++ b/Makefile
+@@ -290,6 +290,7 @@ endif
+
+ ifeq ($(DEBIAN),1)
+ clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro,--enable-new-dtags
++ DISABLE_VECTORIZE_CHECK:=1
+ endif
+
+ ifeq ($(DEBUG),1)
=====================================
debian/patches/130_bundled_raxml_build_c17.patch
=====================================
@@ -0,0 +1,33 @@
+Description: Build bundled RAxML/SATIVA sources as C17
+ GCC 16 defaults to C23, where 'bool' is a keyword and the bundled
+ RAxML8 and SATIVA sources fail to compile ('typedef int bool',
+ implicit function declarations). Build the bundled copies as C17 to
+ keep them compiling.
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-10-23
+Assisted-By: deepseek-v4.1-flash-free
+
+--- a/GDE/RAxML8/Makefile
++++ b/GDE/RAxML8/Makefile
+@@ -55,7 +55,8 @@
+ rm -rf $$DIR &&\
+ mkdir $$DIR &&\
+ tar -C $$DIR --strip-components=1 -xzf $(TARFILE) &&\
+- arb_sed -i 's/-march=native//' $$DIR/Makefile*)
++ arb_sed -i 's/-march=native//' $$DIR/Makefile* &&\
++ arb_sed -i 's/^CFLAGS = /CFLAGS = -std=gnu17 -fcommon -Wno-error=implicit-int -Wno-error=implicit-function-declaration /' $$DIR/Makefile*)
+ touch $@ -r $(TARFILE)
+
+ %.stamp:
+--- a/GDE/SATIVA/Makefile
++++ b/GDE/SATIVA/Makefile
+@@ -64,7 +64,8 @@
+ rm -rf $$DIR &&\
+ mkdir $$DIR &&\
+ tar -C $$DIR --strip-components=1 -xzf $(TARFILE) &&\
+- arb_sed -i 's/-march=native//' $$DIR/Makefile*)
++ arb_sed -i 's/-march=native//' $$DIR/Makefile* &&\
++ arb_sed -i 's/^CFLAGS = /CFLAGS = -std=gnu17 -fcommon -Wno-error=implicit-int -Wno-error=implicit-function-declaration /' $$DIR/Makefile*)
+ touch $@ -r $(TARFILE)
+
+ %.stamp:
=====================================
debian/patches/140_compile_compat_strip_c_std.patch
=====================================
@@ -0,0 +1,29 @@
+Description: Strip C standard from no-standard compatibility build
+ debian/rules adds -std=gnu17 to CFLAGS to build the old C sources as
+ C17 (GCC 16 defaults to C23). ARB passes CFLAGS to C++ compilations as
+ well, so the 'nostd' compatibility target has to remove that option to
+ really build without an explicit C++ standard.
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-10-23
+Assisted-By: deepseek-v4.1-flash-free
+
+--- a/SOURCE_TOOLS/COMPILE_COMPAT/Makefile
++++ b/SOURCE_TOOLS/COMPILE_COMPAT/Makefile
+@@ -30,6 +30,8 @@
+ cxxflags_nostd:=$(subst -std=gnu++11,,$(cxxflags_nostd))
+ cxxflags_nostd:=$(subst -std=gnu++14,,$(cxxflags_nostd))
+ cxxflags_nostd:=$(subst -std=gnu++17,,$(cxxflags_nostd))
++cxxflags_nostd:=$(subst -std=gnu17,,$(cxxflags_nostd))
++cflags_nostd:=$(subst -std=gnu17,,$(cflags))
+
+ disabled_warn_nostd:=-Wno-unused-local-typedefs -Wno-zero-as-null-pointer-constant
+
+@@ -37,7 +39,7 @@
+ $(A_CXX) $(cflags) $(cxxflags_c0x) -c $< $(CXX_INCLUDES) -o $@ $(POST_COMPILE) $<
+
+ nostd.o: nostd.cxx Makefile
+- $(A_CXX) $(cflags) $(cxxflags_nostd) $(disabled_warn_nostd) -c $< $(CXX_INCLUDES) -o $@ $(POST_COMPILE) $<
++ $(A_CXX) $(cflags_nostd) $(cxxflags_nostd) $(disabled_warn_nostd) -c $< $(CXX_INCLUDES) -o $@ $(POST_COMPILE) $<
+
+ bin/% : %.o
+ $(LINK_EXECUTABLE) $@ $< $(LIB_ARBDB)
=====================================
debian/patches/20_upstream_r12794__socket_permissions deleted
=====================================
@@ -1,28 +0,0 @@
-Author: Elmar Pruesse <elmar at pruesse.net>
-Last-Update: 2014-09-02
-Description: backported security fix
-Origin: upstream, http://bugs.arb-home.de/changeset/12794
-
---- a/SH/arb_launcher
-+++ b/SH/arb_launcher
-@@ -296,7 +296,7 @@ create_pipe_reader() {
- trap "term_handler $NAMED_PIPE" TERM
- trap "rm -f $NAMED_PIPE" EXIT
-
-- { mkfifo $NAMED_PIPE && listen_pipe $NAMED_PIPE ; } || \
-+ { mkfifo -m 600 $NAMED_PIPE && listen_pipe $NAMED_PIPE ; } || \
- { echo "Error creating pipe '$NAMED_PIPE'" ; kill $PARENT_PID ; }
-
- debug "Pipe reader for '$NAMED_PIPE' terminates.."
-@@ -325,8 +325,9 @@ wait_for_pipe() {
- }
-
- get_pipe_name() {
-- local SOCKETDIR=$HOME/.arb_tmp/sockets
-- mkdir -p $SOCKETDIR
-+ local SOCKETDIR="$HOME/.arb_tmp/sockets"
-+ mkdir -p "$SOCKETDIR"
-+ chmod 0700 "$SOCKETDIR"
- echo "$SOCKETDIR/arb_launcher.$ARB_PID"
-
- # instead of the above code, use the following to test a pipe-creation failure:
=====================================
debian/patches/30_upstream_r12814__desktop_keywords deleted
=====================================
@@ -1,13 +0,0 @@
-Author: Elmar Pruesse <elmar at pruesse.net>
-Last-Update: 2014-09-02
-Description: add keywords to arb.desktop
-Origin: upstream, http://bugs.arb-home.de/changeset/12814
-
---- a/lib/desktop/arb.desktop
-+++ b/lib/desktop/arb.desktop
-@@ -7,4 +7,4 @@ Categories=Science;Biology
- Terminal=false
- Comment=Visit http://www.arb-home.de
- MimeType=application/x-arb
--
-+Keywords=sequence;phylogeny;dna;rna;taxonomy;gene;16S;SSU;LSU;rRNA;probe design;
=====================================
debian/patches/40_upstream_r12815__lintian_spelling deleted
=====================================
@@ -1,294 +0,0 @@
-Author: Elmar Pruesse <elmar at pruesse.net>
-Last-Update: 2014-09-02
-Description: fix lintian detected spelling errors
-Origin: upstream, http://bugs.arb-home.de/changeset/12815
-
---- a/GDE/CLUSTALW/interface.c
-+++ b/GDE/CLUSTALW/interface.c
-@@ -1372,7 +1372,7 @@ void parse_params(Boolean xmenus)
-
-
- /*****************************************************************************/
--/* Check to see if sequence type is explicitely stated..override ************/
-+/* Check to see if sequence type is explicitly stated..override ************/
- /* the automatic checking (DNA or Protein). /type=d or /type=p *************/
- /*****************************************************************************/
- if(settype != -1)
---- a/GDE/CLUSTAL/amenu.c
-+++ b/GDE/CLUSTAL/amenu.c
-@@ -342,7 +342,7 @@ void parse_params()
-
-
- /*****************************************************************************/
--/* Check to see if sequence type is explicitely stated..override ************/
-+/* Check to see if sequence type is explicitly stated..override ************/
- /* the automatic checking (DNA or Protein). /type=d or /type=p *************/
- /*****************************************************************************/
- if(check_param(params, typest, param_arg, ¶m_arg_len))
-@@ -351,11 +351,11 @@ void parse_params()
- dnaflag = FALSE;
- explicit_dnaflag = TRUE;
- fprintf(stdout,
-- "\nSequence type explicitely set to Protein\n");
-+ "\nSequence type explicitly set to Protein\n");
- }
- else if(param_arg[0] == 'd') {
- fprintf(stdout,
-- "\nSequence type explicitely set to DNA\n");
-+ "\nSequence type explicitly set to DNA\n");
- dnaflag = TRUE;
- explicit_dnaflag = TRUE;
- }
---- a/ARBDB/adGene.cxx
-+++ b/ARBDB/adGene.cxx
-@@ -251,7 +251,7 @@ GEN_position *GEN_read_position(GBDATA *
-
- if (gb_pos_joined) {
- parts = GB_read_int(gb_pos_joined);
-- if (parts != 1) { // splitted
-+ if (parts != 1) { // split
- if (parts>1) joinable = true;
- else if (parts<-1) parts = -parts; // neg value means "not joinable" (comes from feature location 'order(...)')
- else error = GBS_global_string("Illegal value %i in 'pos_joined'", parts);
---- a/ARBDB/adsocket.cxx
-+++ b/ARBDB/adsocket.cxx
-@@ -1356,7 +1356,7 @@ void GB_remove_on_exit(const char *filen
-
- void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix) {
- // Takes a file (or directory) name and splits it into "path/name.suffix".
-- // If result pointers (res_*) are non-NULL, they are assigned heap-copies of the splitted parts.
-+ // If result pointers (res_*) are non-NULL, they are assigned heap-copies of the split parts.
- // If parts are not valid (e.g. cause 'fullpath' doesn't have a .suffix) the corresponding result pointer
- // is set to NULL.
- //
---- a/NTREE/NT_tree_cmp.cxx
-+++ b/NTREE/NT_tree_cmp.cxx
-@@ -145,7 +145,7 @@ AWT_species_set::~AWT_species_set() {
-
- AWT_species_set *AWT_species_set_root::move_tree_2_ssr(AP_tree *node) {
- AWT_species_set *ss;
-- // Warning: confusing ressource handling:
-+ // Warning: confusing resource handling:
- // - leafs are returned "NOT owned by anybody"
- // - inner nodes are added to and owned by this->sets
-
---- a/GENOM/GEN_gene.cxx
-+++ b/GENOM/GEN_gene.cxx
-@@ -37,7 +37,7 @@
- //
- // pos_complement = 1 -> CDS is on opposite strand
-
--// fields for splitted genes:
-+// fields for split genes:
- // --------------------------
- // pos_joined = xxx -> gene consists of abs(xxx) parts (if missing xxx == 1 is assumed)
- //
-@@ -83,7 +83,7 @@
- // pos_uncertain = contains 2 chars (1. for start-pos, 2. for end-pos); = means 'pos is exact'; < means 'pos may be lower'; > means 'pos may be higher'; missing -> like ==
- // complement = 1 -> encoding from right to left
- //
--// fields for splitted genes:
-+// fields for split genes:
- // --------------------------
- // pos_joined = xxx -> gene consists of xxx parts (may not exist if xxx == 1)
- // pos_beginxxx, pos_endxxx = start-/end-positions for parts 2...n
-@@ -138,7 +138,7 @@ GEN_gene::GEN_gene(GBDATA *gb_gene_, GEN
- }
-
- GEN_gene::GEN_gene(GBDATA *gb_gene_, GEN_root *root_, const GEN_position *location, int partNumber) {
-- // partNumber 1..n which part of a splitted gene
-+ // partNumber 1..n which part of a split gene
- // maxParts 1..n of how many parts consists this gene?
-
- init(gb_gene_, root_);
---- a/PRIMER_DESIGN/primer_design.cxx
-+++ b/PRIMER_DESIGN/primer_design.cxx
-@@ -347,7 +347,7 @@ static void primer_design_event_init(AW_
- length = gene_length;
- add_offset = genPos->start_pos[0];
- #if defined(WARN_TODO)
--#warning does this work with splitted genes ?
-+#warning does this work with split genes ?
- #warning warn about uncertainties ?
- #endif
- }
---- a/CORE/arb_strarray.cxx
-+++ b/CORE/arb_strarray.cxx
-@@ -36,7 +36,7 @@ void CharPtrArray::sort(CharPtrArray_com
- void GBT_splitNdestroy_string(ConstStrArray& names, char*& namelist, const char *separator, bool dropEmptyTokens) {
- /*! Split 'namelist' into an array of substrings at each member of 'separator'.
- *
-- * @param names pointers to splitted parts (into namelist)
-+ * @param names pointers to split parts (into namelist)
- * @param namelist string containing separator delimited parts
- * @param separator contains all characters handled as separators
- * @param dropEmptyTokens if true, empty tokens will be skipped
---- a/CORE/arb_progress.h
-+++ b/CORE/arb_progress.h
-@@ -164,7 +164,7 @@ public:
- //
- // expects to be incremented 'overall_count' times
- // incrementation is done either
-- // - explicitely by calling one of the inc...()-functions below or
-+ // - explicitly by calling one of the inc...()-functions below or
- // - implicitely by creating another arb_progress while this one remains
- //
- // if you can't ahead-determine the exact number of incrementations,
-@@ -176,7 +176,7 @@ public:
- explicit arb_progress(const char *title) {
- // open a wrapping progress indicator
- //
-- // expects NOT to be incremented explicitely!
-+ // expects NOT to be incremented explicitly!
- // if arb_progresses are created while this exists, they reuse the progress window.
- // Useful to avoid spamming the user with numerous popping-up progress windows.
- setup(title, 0);
---- a/WINDOW/AW_xfig.cxx
-+++ b/WINDOW/AW_xfig.cxx
-@@ -416,7 +416,7 @@ AW_xfig::AW_xfig(const char *filename, i
- free(buffer);
-
- if (error) {
-- error = GBS_global_string("Error: Can't read XFIG ressource - programmers error or defect installation\n"
-+ error = GBS_global_string("Error: Can't read XFIG resource - programmers error or defect installation\n"
- "Reason: %s\n", error);
-
- if (font_width>0 && font_height>0) { // react with fatal exit
---- a/ARB_GDE/GDE_event.cxx
-+++ b/ARB_GDE/GDE_event.cxx
-@@ -130,7 +130,7 @@ static char *ReplaceArgs(AW_root *awr, c
- }
- else {
- aw_message(GBS_global_string("[ARB_GDE]: Cannot access label of '%s'\n", symbol));
-- return NULL; // @@@ ignores ressources (should only occur during development)
-+ return NULL; // @@@ ignores resources (should only occur during development)
- }
- }
-
---- a/TOOLS/arb_consensus_tree.cxx
-+++ b/TOOLS/arb_consensus_tree.cxx
-@@ -169,7 +169,7 @@ int ARB_main(int argc, char *argv[]) {
- error = save_tree_as_newick(cons_tree, savename, comment);
- }
- else {
-- printf("sucessfully created consensus tree\n"
-+ printf("successfully created consensus tree\n"
- "(no savename specified -> tree not saved)\n");
- }
- delete cons_tree;
---- a/TOOLS/arb_gene_probe.cxx
-+++ b/TOOLS/arb_gene_probe.cxx
-@@ -31,7 +31,7 @@ using namespace std;
- // --------------------------------------------------------------------------------
-
- static int gene_counter = 0; // pre-incremented counters
--static int splitted_gene_counter = 0;
-+static int split_gene_counter = 0;
- static int intergene_counter = 0;
-
- struct nameOrder {
-@@ -299,7 +299,7 @@ static GB_ERROR create_gene(GBDATA *gb_s
- return "Illegal gene positions (start behind end)";
- }
-
--static GB_ERROR create_splitted_gene(GBDATA *gb_species_data2, PositionPairList& part_list, const char *ali_genome, const char *long_gene_name) {
-+static GB_ERROR create_split_gene(GBDATA *gb_species_data2, PositionPairList& part_list, const char *ali_genome, const char *long_gene_name) {
- GB_ERROR error = 0;
- PositionPairList::iterator list_end = part_list.end();
-
-@@ -339,7 +339,7 @@ static GB_ERROR create_splitted_gene(GBD
- }
-
- char internal_name[128];
-- sprintf(internal_name, "s%x", splitted_gene_counter++);
-+ sprintf(internal_name, "s%x", split_gene_counter++);
-
- const PositionPair& first_part = part_list.front();
- GBDATA *gb_species2 = create_gene_species(gb_species_data2, internal_name, long_gene_name, first_part.begin,
-@@ -348,7 +348,7 @@ static GB_ERROR create_splitted_gene(GBD
- if (!gb_species2) error = GB_await_error();
- else {
- #if defined(DEBUG) && 0
-- printf("splitted gene: long_gene_name='%s' internal_name='%s' split_pos_list='%s'\n",
-+ printf("split gene: long_gene_name='%s' internal_name='%s' split_pos_list='%s'\n",
- long_gene_name, internal_name, split_pos_list);
- #endif // DEBUG
- error = GBT_write_string(gb_species2, "splitpos", split_pos_list);
-@@ -386,7 +386,7 @@ static GB_ERROR insert_genes_of_organism
- GenePositionMap geneRanges;
-
- int gene_counter_old = gene_counter; // used for statistics only (see end of function)
-- int splitted_gene_counter_old = splitted_gene_counter;
-+ int split_gene_counter_old = split_gene_counter;
- int intergene_counter_old = intergene_counter;
-
- GBDATA *gb_ali_genom = GBT_read_sequence(gb_organism, GENOM_ALIGNMENT);
-@@ -417,8 +417,8 @@ static GB_ERROR insert_genes_of_organism
- error = create_gene(gb_species_data2, first_part.begin, first_part.end, ali_genom, long_gene_name);
- geneRanges.announceGene(first_part);
- }
-- else { // splitted gene
-- error = create_splitted_gene(gb_species_data2, part_list, ali_genom, long_gene_name);
-+ else { // split gene
-+ error = create_split_gene(gb_species_data2, part_list, ali_genom, long_gene_name);
-
- for (PositionPairList::iterator p = part_list.begin(); p != part_list.end(); ++p) {
- geneRanges.announceGene(*p);
-@@ -447,8 +447,8 @@ static GB_ERROR insert_genes_of_organism
- if (error && organism_name) error = GBS_global_string("in organism '%s': %s", organism_name, error);
-
- {
-- int new_genes = gene_counter-gene_counter_old; // only non-splitted genes
-- int new_splitted_genes = splitted_gene_counter-splitted_gene_counter_old;
-+ int new_genes = gene_counter-gene_counter_old; // only non-split genes
-+ int new_split_genes = split_gene_counter-split_gene_counter_old;
- int new_intergenes = intergene_counter-intergene_counter_old;
-
- unsigned long genesSize = geneRanges.getAllGeneSize();
-@@ -456,10 +456,10 @@ static GB_ERROR insert_genes_of_organism
- double data_grow = overlaps/double(PositionPair::genome_length)*100;
- double gene_overlap = overlaps/double(genesSize)*100;
-
-- if (new_splitted_genes) {
-+ if (new_split_genes) {
-
-- printf(" - %s: %i genes (%i splitted), %i intergenes",
-- organism_name, new_genes+new_splitted_genes, new_splitted_genes, new_intergenes);
-+ printf(" - %s: %i genes (%i split), %i intergenes",
-+ organism_name, new_genes+new_split_genes, new_split_genes, new_intergenes);
- }
- else {
- printf(" - %s: %i genes, %i intergenes",
-@@ -536,8 +536,8 @@ int ARB_main(int argc, char *argv[]) {
-
- if (!error) {
- printf("%i species had data in alignment '" GENOM_ALIGNMENT "'.\n"
-- "Found %i genes (%i were splitted) and %i intergene regions.\n",
-- ali_genom_species, gene_counter, splitted_gene_counter, intergene_counter);
-+ "Found %i genes (%i were split) and %i intergene regions.\n",
-+ ali_genom_species, gene_counter, split_gene_counter, intergene_counter);
- }
-
- if (!error) {
---- a/STAT/st_quality.hxx
-+++ b/STAT/st_quality.hxx
-@@ -64,7 +64,7 @@ public:
- };
-
- class LikelihoodRanges : virtual Noncopyable {
-- /*! The alignment is splitted into multiple, similar-sized column ranges.
-+ /*! The alignment is split into multiple, similar-sized column ranges.
- * For each range the likelihoods get summarized
- */
- size_t ranges;
---- a/SL/FAST_ALIGNER/fast_aligner.cxx
-+++ b/SL/FAST_ALIGNER/fast_aligner.cxx
-@@ -67,7 +67,7 @@ enum FA_turn {
- };
-
- enum FA_reference {
-- FA_REF_EXPLICIT, // reference sequence explicitely specified
-+ FA_REF_EXPLICIT, // reference sequence explicitly specified
- FA_REF_CONSENSUS, // use group consensus as reference
- FA_REF_RELATIVES, // search next relatives by PT server
- };
=====================================
debian/patches/60_use_packaged_phyml
=====================================
@@ -1,6 +1,7 @@
Description: use phyml package instead of version source distributed with ARB
Author: Elmar Pruesse <elmar at pruesse.net>
Origin: other
+Assisted-By: deepseek-v4.1-flash-free
--- a/GDE/Makefile
+++ b/GDE/Makefile
@@ -5,7 +5,6 @@ ARCHS_COMMON_DEPENDS = \
@@ -8,10 +9,10 @@ Origin: other
ARCHS_COMMON_NO_DEPENDS = \
- PHYML20130708/PHYML20130708.dummy \
+ RAxML8/RAxML8.dummy \
+ SATIVA/SATIVA.dummy \
- # --------------------------------------------------------------------------------
- # If a package is available as debian package it should go here
-@@ -26,6 +25,7 @@ ARCHS_NON_DEBIAN_NO_DEPENDS = \
+@@ -29,6 +28,7 @@ ARCHS_NON_DEBIAN_NO_DEPENDS = \
FASTTREE/FASTTREE.dummy \
MAFFT/MAFFT.dummy \
MUSCLE/MUSCLE.dummy \
=====================================
debian/patches/70_skip_compler_version_check.patch
=====================================
@@ -1,11 +1,12 @@
Description: Skip compiler version check at all
Author: Andreas Tille <tille at debian.org>
Bug-Debian: http://bugs.debian.org/793187
-Last-Update: 2015-07-22
+Last-Update: 2026-10-23
+Assisted-By: deepseek-v4.1-flash-free
--- a/Makefile
+++ b/Makefile
-@@ -749,24 +749,7 @@ check_same_GCC_VERSION:
+@@ -1120,30 +1120,7 @@ check_same_GCC_VERSION:
$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
check_GCC_VERSION:
@@ -19,13 +20,19 @@ Last-Update: 2015-07-22
- @echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
- @echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
- @echo ' a different version of gcc)'
-- @echo ''
-- @false
+- $(error Unsupported compiler '$(COMPILER_NAME)' version '$(COMPILER_VERSION)')
-else
+- ifeq ($(COMPILER_BROKEN),1)
+- $(error compilation refused for $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)'. Refer to http://bugs.arb-home.de/wiki/GccVersionInfo for details.)
+- else
- @echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
- @echo ''
+- ifeq ($(USE_CLANG),1)
+- @echo "Dump clang version:"
+- $(A_CXX) -v
+- endif
- $(MAKE) check_same_GCC_VERSION
--
+- endif
-endif
+ @echo 'Skip compiler version check in Debian - we need to fix the code if it does not work'
=====================================
debian/patches/80_enable_new_dtags.patch
=====================================
@@ -1,20 +1,19 @@
Author: From: Tim Booth <avarus at fastmail.fm>
-Last-Update: Mon, 19 Oct 2015 15:30:28 +0100
-Description Apparently back in 1995 the ELF standard was tweaked to handle some
+Last-Update: 2026-10-23
+Assisted-By: deepseek-v4.1-flash-free
+Description: Apparently back in 1995 the ELF standard was tweaked to handle some
crufty behaviour of RPATH - see http://blog.tremily.us/posts/rpath/
but Debian never adopted it. But for this package we do want it, so
add the extra linker flag.
--- a/Makefile
+++ b/Makefile
-@@ -201,8 +201,8 @@ ifeq ($(DEBUG),0)
+@@ -289,7 +289,7 @@
endif
ifeq ($(DEBIAN),1)
-- lflags += -rpath=/usr/lib/arb/lib -z relro
-- clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
-+ lflags += -rpath=/usr/lib/arb/lib -z relro --enable-new-dtags
-+ clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro,--enable-new-dtags
+- clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
++ clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro,--enable-new-dtags
endif
ifeq ($(DEBUG),1)
=====================================
debian/patches/90_do_not_create_MAFFT_symlinks.patch
=====================================
@@ -1,25 +1,24 @@
From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
Date: Tue, 12 Sep 2017 17:04:29 +0200
Subject: do not create MAFFT symlinks
+Assisted-By: deepseek-v4.1-flash-free
---
bin/Makefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
-diff --git a/bin/Makefile b/bin/Makefile
-index 3825a10..26524c2 100644
--- a/bin/Makefile
+++ b/bin/Makefile
-@@ -12,10 +12,10 @@ help:
+@@ -12,10 +12,10 @@
# ----------------------------------------
- all: cleanlinks
+ all: autoremove
- $(MAKE) scriptlinks mafftlinks
+ $(MAKE) scriptlinks
- develall: cleanlinks
+ develall: autoremove
- $(MAKE) scriptlinks mafftlinks devellinks
+ $(MAKE) scriptlinks devellinks
# ----------------------------------------
-
+ # autoremove no-longer-made binaries
=====================================
debian/patches/gcc-16+
=====================================
@@ -1,8 +1,11 @@
+Description: Fix compilation with gcc 16
+Assisted-By: deepseek-v4.1-flash-free
+
Index: arb/PROBE/PT_new_design.cxx
===================================================================
---- arb.orig/PROBE/PT_new_design.cxx
-+++ arb/PROBE/PT_new_design.cxx
-@@ -1235,7 +1235,7 @@ public:
+--- a/PROBE/PT_new_design.cxx
++++ b/PROBE/PT_new_design.cxx
+@@ -1247,7 +1247,7 @@ public:
};
struct SCP_Less {
@@ -11,18 +14,3 @@ Index: arb/PROBE/PT_new_design.cxx
};
class ProbeCandidates {
-Index: arb/GDE/SUPPORT/CAP2.c
-===================================================================
---- arb.orig/GDE/SUPPORT/CAP2.c
-+++ arb/GDE/SUPPORT/CAP2.c
-@@ -284,8 +284,8 @@ char *argv[];
- char *sequence; /* Storing all segments */
- char *reverse; /* Storing all reverse segments */
- int symbol, prev; /* The next character */
-- FILE *Ap, *ckopen(); /* For the sequence file */
-- char *my_calloc(int); /* space-allocating function */
-+ FILE *Ap, *ckopen(char *name, char *mode); /* For the sequence file */
-+ char *my_calloc(int size); /* space-allocating function */
- register int i, j, k; /* index variables */
- /* Mod by S.S. */
- int jj;
=====================================
debian/patches/series
=====================================
@@ -1,7 +1,3 @@
-10_upstream_r12793__show_db_load_progress
-20_upstream_r12794__socket_permissions
-30_upstream_r12814__desktop_keywords
-40_upstream_r12815__lintian_spelling
50_private_nameservers
60_use_packaged_phyml
70_skip_compler_version_check.patch
@@ -11,3 +7,6 @@
110_narrowing.patch
111_fgets.patch
gcc-16+
+120_disable_vectorize_check.patch
+130_bundled_raxml_build_c17.patch
+140_compile_compat_strip_c_std.patch
=====================================
debian/rules
=====================================
@@ -32,6 +32,7 @@ export DEB_CXXFLAGS_MAINT_APPEND=-std=c++98
# function declarations that would normally be fixed with proper header
# files.
export DEB_CFLAGS_MAINT_APPEND=\
+ -std=gnu17 \
-Wno-error=implicit-int \
-Wno-error=implicit-function-declaration
@@ -86,7 +87,7 @@ override_dh_install:
rm -f debian/tmp/arb_OS_X.txt
rm -f debian/tmp/arb_UBUNTU.txt
- dh_install --list-missing
+ dh_install
# the check is needed to make sure it will not fail when doing binary-arch only builds
if [ -e debian/$(pkgcom)/usr/lib/arb/SH/arb_create_debian_conffile ] ; then \
@@ -97,6 +98,9 @@ override_dh_install:
chmod a+x debian/$(pkgcom)/usr/lib/arb/lib/macro.head ; \
fi
+override_dh_missing:
+ dh_missing --list-missing
+
override_dh_strip:
# Fix rpath issue (once libarb is installed)
if [ -e debian/libarb/usr/lib/arb/lib/ARB.so ] ; then \
View it on GitLab: https://salsa.debian.org/med-team/arb/-/compare/07e9e04b99fd928c7336b0a6bf2e7d83a2d283dc...488efa9f1d302be402b0eeff2e8321744a68ab94
--
View it on GitLab: https://salsa.debian.org/med-team/arb/-/compare/07e9e04b99fd928c7336b0a6bf2e7d83a2d283dc...488efa9f1d302be402b0eeff2e8321744a68ab94
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