[med-svn] r17921 - trunk/packages/arb/trunk/debian/patches
Elmar Pruesse
epruesse-guest at moszumanska.debian.org
Tue Sep 2 17:02:43 UTC 2014
Author: epruesse-guest
Date: 2014-09-02 17:02:43 +0000 (Tue, 02 Sep 2014)
New Revision: 17921
Added:
trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling
Modified:
trunk/packages/arb/trunk/debian/patches/series
Log:
add patches to fix lintian warnings
Added: trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling
===================================================================
--- trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/40_upstream_r12815__lintian_spelling 2014-09-02 17:02:43 UTC (rev 17921)
@@ -0,0 +1,240 @@
+Author: Elmar Pruesse <elmar at pruesse.net>
+Last-Update: Tue, 02 Sep 2014 17:56:47 +0200
+Description: backported patch fixing lintian detected spelling errors
+
+--- a/GDE/CLUSTALW/interface.c
++++ b/GDE/CLUSTALW/interface.c
+@@ -1373,5 +1373,5 @@
+
+ /*****************************************************************************/
+-/* 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 *************/
+ /*****************************************************************************/
+--- a/GDE/CLUSTAL/amenu.c
++++ b/GDE/CLUSTAL/amenu.c
+@@ -343,5 +343,5 @@
+
+ /*****************************************************************************/
+-/* 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 @@
+ 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
+@@ -252,5 +252,5 @@
+ 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(...)')
+--- a/ARBDB/adsocket.cxx
++++ b/ARBDB/adsocket.cxx
+@@ -1222,5 +1222,5 @@
+ 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 @@
+ 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 @@
+ // 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 @@
+ // 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 @@
+
+ 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?
+
+--- a/PRIMER_DESIGN/primer_design.cxx
++++ b/PRIMER_DESIGN/primer_design.cxx
+@@ -348,5 +348,5 @@
+ 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 @@
+ /*! 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
+--- a/CORE/arb_progress.h
++++ b/CORE/arb_progress.h
+@@ -165,5 +165,5 @@
+ // 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 @@
+ // 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.
+--- a/WINDOW/AW_xfig.cxx
++++ b/WINDOW/AW_xfig.cxx
+@@ -417,5 +417,5 @@
+
+ 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);
+
+--- a/ARB_GDE/GDE_event.cxx
++++ b/ARB_GDE/GDE_event.cxx
+@@ -130,5 +130,5 @@
+ 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 @@
+ }
+ else {
+- printf("sucessfully created consensus tree\n"
++ printf("successfully created consensus tree\n"
+ "(no savename specified -> tree not saved)\n");
+ }
+--- a/TOOLS/arb_gene_probe.cxx
++++ b/TOOLS/arb_gene_probe.cxx
+@@ -32,5 +32,5 @@
+
+ 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 @@
+ }
+
+-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 @@
+
+ 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 @@
+ 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 @@
+
+ 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 @@
+ 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) {
+@@ -448,6 +448,6 @@
+
+ {
+- 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;
+
+@@ -457,8 +457,8 @@
+ double gene_overlap = overlaps/double(genesSize)*100;
+
+- if (new_splitted_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 @@
+ 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);
+ }
+
+--- a/STAT/st_quality.hxx
++++ b/STAT/st_quality.hxx
+@@ -65,5 +65,5 @@
+
+ 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
+ */
+--- a/SL/FAST_ALIGNER/fast_aligner.cxx
++++ b/SL/FAST_ALIGNER/fast_aligner.cxx
+@@ -68,5 +68,5 @@
+
+ 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/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2014-09-02 16:55:25 UTC (rev 17920)
+++ trunk/packages/arb/trunk/debian/patches/series 2014-09-02 17:02:43 UTC (rev 17921)
@@ -1,2 +1,4 @@
10_upstream_r12793__show_db_load_progress
20_upstream_r12794__socket_permissions
+30_upstream_r12814__desktop_keywords
+40_upstream_r12815__lintian_spelling
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