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Fix build for LDC 1.26.0 and LLVM 9.0.1 - tests pass

master
Pjotr Prins 3 months ago
parent
commit
931fcc1ee2
  1. 3
      .guix-build
  2. 7
      INSTALL.md
  3. 4
      Makefile.guix
  4. 1
      RELEASE-NOTES.md
  5. 2
      VERSION
  6. 1
      sambamba/pileup.d
  7. 4
      test/test_suite.sh

3
.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 $*

7
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.

4
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:

1
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)

2
VERSION

@ -1 +1 @@
0.8.0
0.8.1-pre1

1
sambamba/pileup.d

@ -749,4 +749,5 @@ int pileup_main(string[] args) {
return 1;
}
}
return 0;
}

4
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

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