[med-svn] r20706 - in trunk/packages/arb/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Thu Dec 10 11:17:06 UTC 2015
Author: tille
Date: 2015-12-10 11:17:05 +0000 (Thu, 10 Dec 2015)
New Revision: 20706
Added:
trunk/packages/arb/trunk/debian/patches/80_enable_new_dtags.patch
Modified:
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/patches/30_upstream_r12814__desktop_keywords
trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling
trunk/packages/arb/trunk/debian/patches/50_private_nameservers
trunk/packages/arb/trunk/debian/patches/60_use_packaged_phyml
trunk/packages/arb/trunk/debian/patches/70_skip_compler_version_check.patch
trunk/packages/arb/trunk/debian/patches/series
trunk/packages/arb/trunk/debian/watch
Log:
New upstream version with adapted patches, extra linker flag proposed by Tim Booth
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/changelog 2015-12-10 11:17:05 UTC (rev 20706)
@@ -1,5 +1,6 @@
-arb (6.0.2-3) UNRELEASED; urgency=medium
+arb (6.0.3-1) UNRELEASED; urgency=medium
+ * New upstream version
* Applied all l10n patches - thanks a lot for the great l10n team
for pushing this
* Debconf templates and debian/control reviewed by the debian-l10n-
@@ -16,8 +17,9 @@
* French (Steve Petruzzello). Closes: #766728
* Catalan; (Innocent De Marchi). Closes: #766855
* Japanese (Hideki Yamane (Debian-JP)). Closes: #767247
+ * extra linker flag proposed by Tim Booth
- -- Andreas Tille <tille at debian.org> Thu, 10 Dec 2015 11:14:14 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 10 Dec 2015 11:29:15 +0100
arb (6.0.2-2) unstable; urgency=medium
Modified: trunk/packages/arb/trunk/debian/patches/30_upstream_r12814__desktop_keywords
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_upstream_r12814__desktop_keywords 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/patches/30_upstream_r12814__desktop_keywords 2015-12-10 11:17:05 UTC (rev 20706)
@@ -5,7 +5,8 @@
--- a/lib/desktop/arb.desktop
+++ b/lib/desktop/arb.desktop
-@@ -8,3 +8,3 @@
+@@ -7,4 +7,4 @@ Categories=Science;Biology
+ Terminal=false
Comment=Visit http://www.arb-home.de
MimeType=application/x-arb
-
Modified: trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling
===================================================================
--- trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling 2015-12-10 11:17:05 UTC (rev 20706)
@@ -5,23 +5,28 @@
--- a/GDE/CLUSTALW/interface.c
+++ b/GDE/CLUSTALW/interface.c
-@@ -1373,5 +1373,5 @@
+@@ -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
-@@ -343,5 +343,5 @@
+@@ -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 *************/
/*****************************************************************************/
-@@ -352,9 +352,9 @@
+ 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");
@@ -33,155 +38,193 @@
+ "\nSequence type explicitly set to DNA\n");
dnaflag = TRUE;
explicit_dnaflag = TRUE;
+ }
--- a/ARBDB/adGene.cxx
+++ b/ARBDB/adGene.cxx
-@@ -252,5 +252,5 @@
+@@ -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
-@@ -1222,5 +1222,5 @@
+@@ -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
-@@ -146,5 +146,5 @@
+@@ -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
-@@ -38,5 +38,5 @@
+@@ -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)
-@@ -84,5 +84,5 @@
+ //
+@@ -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)
-@@ -139,5 +139,5 @@
+ // 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
-@@ -348,5 +348,5 @@
+@@ -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
-@@ -37,5 +37,5 @@
+@@ -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
-@@ -165,5 +165,5 @@
+@@ -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
//
-@@ -177,5 +177,5 @@
+ // 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
-@@ -417,5 +417,5 @@
+@@ -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
-@@ -130,5 +130,5 @@
+@@ -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
-@@ -170,5 +170,5 @@
+@@ -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
-@@ -32,5 +32,5 @@
+@@ -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;
-@@ -300,5 +300,5 @@
+ 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();
-@@ -340,5 +340,5 @@
+@@ -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();
-@@ -349,5 +349,5 @@
+ 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
-@@ -387,5 +387,5 @@
+ 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;
-@@ -418,6 +418,6 @@
+ 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
@@ -190,7 +233,9 @@
+ 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) {
-@@ -448,6 +448,6 @@
+ 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
@@ -199,20 +244,23 @@
+ int new_split_genes = split_gene_counter-split_gene_counter_old;
int new_intergenes = intergene_counter-intergene_counter_old;
-@@ -457,8 +457,8 @@
+ 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);
-+ if (new_split_genes) {
-+
+ printf(" - %s: %i genes (%i split), %i intergenes",
+ organism_name, new_genes+new_split_genes, new_split_genes, new_intergenes);
}
else {
-@@ -537,6 +537,6 @@
+ 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",
@@ -221,21 +269,26 @@
+ ali_genom_species, gene_counter, split_gene_counter, intergene_counter);
}
+ if (!error) {
--- a/STAT/st_quality.hxx
+++ b/STAT/st_quality.hxx
-@@ -65,5 +65,5 @@
+@@ -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
-@@ -68,5 +68,5 @@
+@@ -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
+ };
Modified: trunk/packages/arb/trunk/debian/patches/50_private_nameservers
===================================================================
--- trunk/packages/arb/trunk/debian/patches/50_private_nameservers 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/patches/50_private_nameservers 2015-12-10 11:17:05 UTC (rev 20706)
@@ -10,7 +10,7 @@
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/lib/arb_tcp_org.dat
+++ b/lib/arb_tcp_org.dat
-@@ -56,8 +56,8 @@
+@@ -56,8 +56,8 @@ ARB_DB_SERVER :/tmp/arb_db_$(U
# You may define additional nameservers, using one additional field for identification.
# The defined nameserver 'ARB_NAME_SERVER_START' uses the fields 'acc' and 'start'.
@@ -21,7 +21,7 @@
# ARB_NAME_SERVER_STRAIN localhost:3022 arb_name_server -d$(ARBHOME)/lib/nas/names_strain.dat -fstrain=
# ARB_NAME_SERVER_POS_START localhost:3023 arb_name_server -d$(ARBHOME)/lib/nas/names_pos_start.dat -fpos_start=1
-@@ -73,8 +73,4 @@
+@@ -73,8 +73,4 @@ ARB_PT_SERVER2 localhost:3032
ARB_PT_SERVER3 :$(HOME)/.arb_pts/$(USER)1.socket arb_pt_server -D$(HOME)/.arb_pts/$(USER)1.arb
ARB_PT_SERVER4 :$(HOME)/.arb_pts/$(USER)2.socket arb_pt_server -D$(HOME)/.arb_pts/$(USER)2.arb
ARB_PT_SERVER5 :$(HOME)/.arb_pts/$(USER)3.socket arb_pt_server -D$(HOME)/.arb_pts/$(USER)3.arb
Modified: trunk/packages/arb/trunk/debian/patches/60_use_packaged_phyml
===================================================================
--- trunk/packages/arb/trunk/debian/patches/60_use_packaged_phyml 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/patches/60_use_packaged_phyml 2015-12-10 11:17:05 UTC (rev 20706)
@@ -3,7 +3,7 @@
Origin: other
--- a/GDE/Makefile
+++ b/GDE/Makefile
-@@ -5,7 +5,6 @@
+@@ -5,7 +5,6 @@ ARCHS_COMMON_DEPENDS = \
AxML/AxML.dummy \
ARCHS_COMMON_NO_DEPENDS = \
@@ -11,7 +11,7 @@
# --------------------------------------------------------------------------------
# If a package is available as debian package it should go here
-@@ -26,6 +25,7 @@
+@@ -26,6 +25,7 @@ ARCHS_NON_DEBIAN_NO_DEPENDS = \
FASTTREE/FASTTREE.dummy \
MAFFT/MAFFT.dummy \
MUSCLE/MUSCLE.dummy \
Modified: trunk/packages/arb/trunk/debian/patches/70_skip_compler_version_check.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/70_skip_compler_version_check.patch 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/patches/70_skip_compler_version_check.patch 2015-12-10 11:17:05 UTC (rev 20706)
@@ -5,7 +5,7 @@
--- a/Makefile
+++ b/Makefile
-@@ -736,23 +736,7 @@ check_same_GCC_VERSION:
+@@ -738,23 +738,7 @@ check_same_GCC_VERSION:
$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
check_GCC_VERSION:
Added: trunk/packages/arb/trunk/debian/patches/80_enable_new_dtags.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/80_enable_new_dtags.patch (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/80_enable_new_dtags.patch 2015-12-10 11:17:05 UTC (rev 20706)
@@ -0,0 +1,20 @@
+Author: From: Tim Booth <avarus at fastmail.fm>
+Last-Update: Mon, 19 Oct 2015 15:30:28 +0100
+Description Apparently back in 1995 the ELF standard was tweaked to handle some
+ crufty behaviour of RPATH - see http://blog.tremily.us/posts/rpath/
+ but Debian never adopted it. But for this package we do want it, so
+ add the extra linker flag.
+
+--- a/Makefile
++++ b/Makefile
+@@ -198,8 +198,8 @@ ifeq ($(DEBUG),0)
+ endif
+
+ ifeq ($(DEBIAN),1)
+- lflags += -rpath=/usr/lib/arb/lib -z relro
+- clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
++ lflags += -rpath=/usr/lib/arb/lib -z relro --enable-new-dtags
++ clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro,--enable-new-dtags
+ endif
+
+ ifeq ($(DEBUG),1)
Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/patches/series 2015-12-10 11:17:05 UTC (rev 20706)
@@ -5,3 +5,4 @@
50_private_nameservers
60_use_packaged_phyml
70_skip_compler_version_check.patch
+80_enable_new_dtags.patch
Modified: trunk/packages/arb/trunk/debian/watch
===================================================================
--- trunk/packages/arb/trunk/debian/watch 2015-12-10 10:20:45 UTC (rev 20705)
+++ trunk/packages/arb/trunk/debian/watch 2015-12-10 11:17:05 UTC (rev 20706)
@@ -4,6 +4,3 @@
opts="downloadurlmangle=s{([\d.]+)/$}{$1/arb-$1-source.tgz},filenamemangle=s/\/$/.tgz/" \
http://download.arb-home.de/release/ arb-(\d+.*)/
-
-#opts=downloadurlmangle=s{([\d.]+)/$}{$1/ssake_v$1-tar.gz};s{_v(\d)\.(\d)\.}{_v$1-$2-}g,filenamemangle=s{.+/([\d.]+)$}{ssake_$1.tar.gz} \
-# http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/([\d.]*)
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