[med-svn] [Git][med-team/vt][master] 4 commits: d/control Add missing dependency on r-base-core

[Antoni Villalonga]

Antoni Villalonga pushed to branch master at Debian Med / vt


Commits:
5ec43202 by Antoni Villalonga at 2020-06-17T10:31:36+02:00
d/control Add missing dependency on r-base-core

- - - - -
950e7d4c by Antoni Villalonga at 2020-06-17T11:04:35+02:00
Makefile use env CXXFLAGS to pass blhc tests

- - - - -
5fbf3eeb by Antoni Villalonga at 2020-06-18T09:12:38+02:00
Adapted to recent versions of external libs and warn on test errors

- - - - -
767b74bc by Antoni Villalonga at 2020-06-18T09:16:23+02:00
Update changelog

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/makefile
- debian/patches/series
- + debian/patches/test-fail-on-error


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+vt (0.57721-2) UNRELEASED; urgency=medium
+
+  * d/control Add missing dependency on r-base-core
+  * Makefile use env CXXFLAGS to pass blhc tests
+  * Adapted to recent versions of external libs and warn on test errors
+
+ -- Antoni Villalonga <antoni at friki.cat>  Thu, 18 Jun 2020 09:12:40 +0200
+
 vt (0.57721-1) unstable; urgency=medium
 
   * Initial release


=====================================
debian/control
=====================================
@@ -23,7 +23,9 @@ Rules-Requires-Root: no
 
 Package: vt
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         r-base-core,
 Description: Tool set for short variant discovery in genetic sequence data
  vt is a variant tool set that discovers short variants from Next Generation
  Sequencing data.


=====================================
debian/patches/makefile
=====================================
@@ -1,20 +1,19 @@
 Description: Build again external/system libs
-	Remove local libs
+  Migration from 1.8 to 1.10 libhts
 Author: Antoni Villalonga i Noceras <antoni at friki.cat>
-Last-Update: Wed, 17 Jun 2020 03:31:27 +0200
+Last-Update: Wed, 18 Jun 2020 09:10:04 +0200
 --- a/Makefile
 +++ b/Makefile
-@@ -1,6 +1,7 @@
+@@ -1,6 +1,6 @@
  OPTFLAG = -O3
 -INCLUDES = -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2
 -CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS
 +INCLUDES = -I. -I/usr/share/R/include
-+CXXFLAGS += $$(CXXFLAGS)
-+CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8
++CXXFLAGS += -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8
  CXX = g++
  
  SOURCESONLY =
-@@ -139,52 +140,26 @@
+@@ -139,52 +139,26 @@
  TARGET = vt
  TOOLSRC = $(SOURCES:=.cpp) $(SOURCESONLY)
  TOOLOBJ = $(TOOLSRC:.cpp=.o)
@@ -86,7 +85,7 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200
                  if (i==buffer.end())
                  {
 -                    int32_t cutoff_pos1 =  std::max(bcf_get_pos1(buffer.front())-window,1);
-+                    int32_t cutoff_pos1 =  std::max((int)bcf_get_pos1(buffer.front())-window,1);
++                    int32_t cutoff_pos1 =  std::max((int32_t)bcf_get_pos1(buffer.front())-window,1);
                      if (bcf_get_pos1(v)<cutoff_pos1)
                      {
                          fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n",
@@ -95,7 +94,7 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200
          if (buffer.size()>1)
          {
 -            int32_t cutoff_pos1 =  std::max(bcf_get_pos1(buffer.front())-window,1);
-+            int32_t cutoff_pos1 =  std::max((int)bcf_get_pos1(buffer.front())-window,1);
++            int32_t cutoff_pos1 =  std::max((int32_t)bcf_get_pos1(buffer.front())-window,1);
  
              while (buffer.size()>1)
              {
@@ -233,3 +232,25 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200
  #include "candidate_region_extractor.h"
  #include "candidate_motif_picker.h"
  #include "flank_detector.h"
+--- a/hts_utils.h
++++ b/hts_utils.h
+@@ -40,9 +40,11 @@
+  *FAI UTILS
+  **********/
+ typedef struct {
++    int id; // faidx_t->name[id] is for this struct.
+     int32_t line_len, line_blen;
+     int64_t len;
+     uint64_t offset;
++    uint64_t qual_offset;
+ } faidx1_t;
+ 
+ KHASH_MAP_INIT_STR(s, faidx1_t)
+@@ -52,6 +54,7 @@
+     int n, m;
+     char **name;
+     khash_t(s) *hash;
++    enum fai_format_options format;
+ };
+ 
+ /**


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 makefile
 fix-spelling
+test-fail-on-error


=====================================
debian/patches/test-fail-on-error
=====================================
@@ -0,0 +1,8 @@
+--- a/test/test.sh
++++ b/test/test.sh
+@@ -235,3 +235,5 @@
+ echo -n ${PASSED_TESTS}  
+ echo -n " / "
+ echo ${NO_TESTS}  
++
++[ ${PASSED_TESTS} -eq  ${NO_TESTS} ]



View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da

-- 
View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da
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