[med-svn] [Git][med-team/genomethreader][master] update patches

[Sascha Steinbiss]

Sascha Steinbiss pushed to branch master at Debian Med / genomethreader


Commits:
cb8612e3 by Sascha Steinbiss at 2020-01-06T23:45:52+01:00
update patches

- - - - -


2 changed files:

- debian/patches/debian-gt-libs.patch
- debian/patches/gt-path-fix.patch


Changes:

=====================================
debian/patches/debian-gt-libs.patch
=====================================
@@ -1,6 +1,6 @@
 --- a/Makefile
 +++ b/Makefile
-@@ -15,19 +15,16 @@
+@@ -15,19 +15,17 @@
  # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  #
  
@@ -11,6 +11,7 @@
 -            -I$(CURDIR)/../genometools/src/external/lua-5.1.5/src \
 +INCLUDEOPT:=-I/usr/include/genometools \
 +	    -I/usr/include/vmatch \
++	    -I/usr/include/lua5.1 \
              -I$(CURDIR)/src -I$(CURDIR)/obj \
  # these variables are exported by the configuration script
 -CC:=gcc
@@ -24,7 +25,7 @@
  
  ifneq ($(fpic),no)
    FPIC:=-fPIC
-@@ -130,11 +127,11 @@
+@@ -130,11 +128,11 @@
  GTMAIN_DEP:=$(GTMAIN_SRC:%.c=obj/%.d)
  
  VSTREEDIR:=../vstree/src
@@ -41,7 +42,7 @@
  GTH_CPPFLAGS+=-I$(CURDIR)/$(VSTREEDIR)/include \
               -I$(CURDIR)/$(VSTREEDIR)/Vmatch \
  
-@@ -209,7 +206,7 @@
+@@ -209,7 +207,7 @@
  all: lib/libgenomethreader.a bin/gth bin/gthconsensus bin/gthbssmfileinfo \
       bin/gthbssmbuild bin/gthbssmprint bin/gthbssmrmsd bin/gthbssmtrain \
       bin/gthfilestat bin/gthmkbssmfiles bin/gthsplit bin/gthunit \
@@ -50,7 +51,7 @@
  
  lib/libgenomethreader.a: obj/gth_config.h $(LIBGENOMETHREADER_OBJ)
  	@echo "[link $(@F)]"
-@@ -231,67 +228,67 @@
+@@ -231,67 +229,67 @@
  $(1): $(2)
  	@echo "[link $$(@F)]"
  	@test -d $$(@D) || mkdir -p $$(@D)
@@ -136,7 +137,7 @@
  
  obj/gth_config.h: VERSION
  	@echo '[create $@]'
-@@ -321,9 +318,9 @@
+@@ -321,9 +319,9 @@
  $(1): $(2)
  	@echo "[compile $$(@F)]"
  	@test -d $$(@D) || mkdir -p $$(@D)
@@ -148,7 +149,7 @@
          $(3) -MM -MP -MT $$@
  endef
  
-@@ -332,17 +329,17 @@
+@@ -332,17 +330,17 @@
  obj/%.o: %.cxx
  	@echo "[compile $(@F)]"
  	@test -d $(@D) || mkdir -p $(@D)


=====================================
debian/patches/gt-path-fix.patch
=====================================
@@ -307,3 +307,14 @@
               "#{$gthtestdata}ngasp/test_ref2.gff3 " +
               "#{$gthtestdata}ngasp/ngasp.gff3", :maxtime => 300
      run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/ngasp.specificity"
+--- a/Makefile
++++ b/Makefile
+@@ -517,7 +517,7 @@
+                           -gtdonor -agacceptor -gzip
+ 	@touch $@
+ 
+-obj/old_train: ../genometools/bin/gt
++obj/old_train: bin/gthmkbssmfiles
+ 	@echo "[write old BSSMs]"
+ 	@bin/gthmkbssmfiles bin/bssm
+ 	@touch $@



View it on GitLab: https://salsa.debian.org/med-team/genomethreader/commit/cb8612e35a7605a701ac0350717cdb79394b1686

-- 
View it on GitLab: https://salsa.debian.org/med-team/genomethreader/commit/cb8612e35a7605a701ac0350717cdb79394b1686
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200106/c6715563/attachment-0001.html>