Fix build for LDC 1.26.0 and LLVM 9.0.1 - tests pass

biod · Jul 31, 2021 · cdb73f5 · cdb73f5
1 parent 67c7351
commit cdb73f5
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Showing 7 changed files with 14 additions and 8 deletions.
diff --git a/.guix-build b/.guix-build
@@ -1,3 +1,4 @@
 # This command creates a build container for Sambamba using GNU Guix
 
-guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib
+env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics \
+guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib $*
diff --git a/INSTALL.md b/INSTALL.md
@@ -18,7 +18,7 @@ and run our development setup (gold was added lately by ldc)
 
     guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim
     make clean
-    make -f Makefile.guix -j 4
+    env CC=gcc make -f Makefile.guix -j 4
     make -f Makefile.guix check
 
 this way all dependencies are isolated. To create a static release use
@@ -31,7 +31,10 @@ We use GNU Guix containers for development. Install Guix and run a build
 container with
 
     . .guix-build
-    make -f Makefile.guix
+    make -f Makefile.guix clean
+    # build the debug version
+    env CC=gcc make -f Makefile.guix lz4-static -j 8
+    env CC=gcc make -f Makefile.guix -j 8
     make -f Makefile.guix check
 
 Note that this also works in the emacs shell.

diff --git a/Makefile.guix b/Makefile.guix
@@ -31,7 +31,7 @@ LIBS   = -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz lz4/lib/liblz4.a
 
 LIBS_STATIC = $(DLIBS) lz4/lib/liblz4.a
 SRC         = $(wildcard main.d utils/*.d thirdparty/*.d) $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d BioD/bio/*/*/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
-OBJ    = $(SRC:.d=.o) utils/ldc_version_info_.o
+OBJ    = $(SRC:.d=.o)
 OUT    = bin/sambamba-$(shell cat VERSION)
 static: OUT += -static
 
@@ -116,7 +116,7 @@ clean-c:
 	rm -v lz4/lib/*.[oa]
 
 clean-d:
-	rm -v $(OBJ) $(OUT) trace.{def,log}
+	rm -v $(OBJ) $(OUT) # trace.{def,log}
 	rm -v bin/*
 
 clean-tests:

diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -2,6 +2,7 @@
 
 + Some FASTA unittests break when they write to disk and read after -
   marked with ~version(Broken)~
++ Fix build for LDC 1.26.0 and LLVM 9.0.1
 
 ## ChangeLog v0.8.0 (20201130)
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.8.0
+0.8.1-pre1
diff --git a/sambamba/pileup.d b/sambamba/pileup.d
@@ -749,4 +749,5 @@ int pileup_main(string[] args) {
           return 1;
         }
     }
+    return 0;
 }
diff --git a/test/test_suite.sh b/test/test_suite.sh
@@ -5,7 +5,7 @@ sambamba=$1
 if [ ! -f $sambamba ]; then
     sambamba=./bin/sambamba
 fi
-opts="-q"
+opts="-q --DRT-testmode=run-main"
 outdir=output
 mkdir -p $outdir
 
@@ -207,7 +207,7 @@ testIssue356(){
     assertEquals 0 $?
 }
 
-testIssue421(){ 
+testIssue421(){
     # sambamba-markdup: not enough data in stream https://github.com/biod/sambamba/issues/421
     cat test/issue_204.bam | $sambamba $opts markdup /dev/stdin test.bam 2> /dev/null
     # assertEquals 0 $?  Disable test until we have a single pass, see issue 421
-Original file line number
+Diff line change
@@ Expand Up / @@ -749,4 +749,5 @@ int pileup_main(string[] args) { @@
               return 1;
             }
         }
+        return 0;
     }