Control: tags -1 help
Hi,
On Mon, Aug 03, 2020 at 10:06:32AM +0200, Lucas Nussbaum wrote:
> > lto1: fatal error: bytecode stream in file
> > ‘/usr/lib/x86_64-linux-gnu/libhts.a’ generated with GCC compiler older than
> > 10.0
I've uploaded a new htslib that is now build with GCC 10 and used a
versioned Build-Depends inside sambamba. Now the build issue changed
to:
[38/41] ldc2 -enable-color -O -g -release -wi -I/usr/include/x86_64-linux-gnu
-I/usr/include/d/bio -O3 -release -enable-inlining -boundscheck=off -J../ -I=..
-I=. -I=sambamba.p -I=sambamba.p
-of=sambamba.p/_build_sambamba-0.7.1_obj-x86_64-linux-gnu_utils_ldc_version_info_.d.o
-c /build/sambamba-0.7.1/obj-x86_64-linux-gnu/utils/ldc_version_info_.d
[39/41] ldc2 -enable-color -O -g -release -wi -I/usr/include/x86_64-linux-gnu
-I/usr/include/d/bio -O3 -release -enable-inlining -boundscheck=off -J../ -I=..
-I=. -I=sambamba.p -I=sambamba.p -of=sambamba.p/thirdparty_unstablesort.d.o -c
../thirdparty/unstablesort.d
[40/41] ldc2 -enable-color -O -g -release -wi -I/usr/include/x86_64-linux-gnu
-I/usr/include/d/bio -O3 -release -enable-inlining -boundscheck=off -J../ -I=..
-I=. -I=sambamba.p -I=sambamba.p -of=sambamba.p/sambamba_view.d.o -c
../sambamba/view.d
[41/41] ldc2 -of=sambamba sambamba.p/sambamba_main.d.o
sambamba.p/sambamba_depth.d.o sambamba.p/sambamba_fixbins.d.o
sambamba.p/sambamba_flagstat.d.o sambamba.p/sambamba_index.d.o
sambamba.p/sambamba_markdup2.d.o sambamba.p/sambamba_markdup.d.o
sambamba.p/sambamba_merge.d.o sambamba.p/sambamba_pileup.d.o
sambamba.p/sambamba_slice.d.o sambamba.p/sambamba_sort.d.o
sambamba.p/sambamba_subsample.d.o sambamba.p/sambamba_utils_common_bed.d.o
sambamba.p/sambamba_utils_common_file.d.o
sambamba.p/sambamba_utils_common_filtering.d.o
sambamba.p/sambamba_utils_common_intervaltree.d.o
sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o
sambamba.p/sambamba_utils_common_overwrite.d.o
sambamba.p/sambamba_utils_common_pratt_parser.d.o
sambamba.p/sambamba_utils_common_progressbar.d.o
sambamba.p/sambamba_utils_common_queryparser.d.o
sambamba.p/sambamba_utils_common_readstorage.d.o
sambamba.p/sambamba_utils_common_tmpdir.d.o
sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o
sambamba.p/sambamba_utils_view_headerserializer.d.o
sambamba.p/sambamba_validate.d.o sambamba.p/sambamba_view.d.o
sambamba.p/utils_lz4.d.o sambamba.p/utils_strip_bcf_header.d.o
sambamba.p/utils_version_.d.o sambamba.p/cram_exception.d.o
sambamba.p/cram_htslib.d.o sambamba.p/cram_reader.d.o
sambamba.p/cram_reference.d.o sambamba.p/cram_slicereader.d.o
sambamba.p/cram_wrappers.d.o sambamba.p/cram_writer.d.o
sambamba.p/thirdparty_mergesort.d.o sambamba.p/thirdparty_unstablesort.d.o
sambamba.p/_build_sambamba-0.7.1_obj-x86_64-linux-gnu_utils_ldc_version_info_.d.o
-L=--allow-shlib-undefined -link-defaultlib-shared -O -g -release -wi -L=-z
-L=relro -L=/usr/lib/x86_64-linux-gnu/libbiod.a
-L=/usr/lib/x86_64-linux-gnu/libz.a -L=/usr/lib/x86_64-linux-gnu/libhts.a -L=-z
-L=relro -L=-z -L=now -L=-flto -fvisibility=hidden
-L=/usr/lib/x86_64-linux-gnu/libbz2.a -L=/usr/lib/x86_64-linux-gnu/libdeflate.a
-L=-lm -L=-lpthread -L=/usr/lib/x86_64-linux-gnu/liblzma.a
/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/liblz4.so
/usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libcrypto.so
/usr/lib/x86_64-linux-gnu/liblzma.so -L=-rpath
-L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu
-L=-rpath-link -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu
-L=-rpath-link -L=/usr/lib/x86_64-linux-gnu
FAILED: sambamba
ldc2 -of=sambamba sambamba.p/sambamba_main.d.o sambamba.p/sambamba_depth.d.o
sambamba.p/sambamba_fixbins.d.o sambamba.p/sambamba_flagstat.d.o
sambamba.p/sambamba_index.d.o sambamba.p/sambamba_markdup2.d.o
sambamba.p/sambamba_markdup.d.o sambamba.p/sambamba_merge.d.o
sambamba.p/sambamba_pileup.d.o sambamba.p/sambamba_slice.d.o
sambamba.p/sambamba_sort.d.o sambamba.p/sambamba_subsample.d.o
sambamba.p/sambamba_utils_common_bed.d.o
sambamba.p/sambamba_utils_common_file.d.o
sambamba.p/sambamba_utils_common_filtering.d.o
sambamba.p/sambamba_utils_common_intervaltree.d.o
sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o
sambamba.p/sambamba_utils_common_overwrite.d.o
sambamba.p/sambamba_utils_common_pratt_parser.d.o
sambamba.p/sambamba_utils_common_progressbar.d.o
sambamba.p/sambamba_utils_common_queryparser.d.o
sambamba.p/sambamba_utils_common_readstorage.d.o
sambamba.p/sambamba_utils_common_tmpdir.d.o
sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o
sambamba.p/sambamba_utils_view_headerserializer.d.o
sambamba.p/sambamba_validate.d.o sambamba.p/sambamba_view.d.o
sambamba.p/utils_lz4.d.o sambamba.p/utils_strip_bcf_header.d.o
sambamba.p/utils_version_.d.o sambamba.p/cram_exception.d.o
sambamba.p/cram_htslib.d.o sambamba.p/cram_reader.d.o
sambamba.p/cram_reference.d.o sambamba.p/cram_slicereader.d.o
sambamba.p/cram_wrappers.d.o sambamba.p/cram_writer.d.o
sambamba.p/thirdparty_mergesort.d.o sambamba.p/thirdparty_unstablesort.d.o
sambamba.p/_build_sambamba-0.7.1_obj-x86_64-linux-gnu_utils_ldc_version_info_.d.o
-L=--allow-shlib-undefined -link-defaultlib-shared -O -g -release -wi -L=-z
-L=relro -L=/usr/lib/x86_64-linux-gnu/libbiod.a
-L=/usr/lib/x86_64-linux-gnu/libz.a -L=/usr/lib/x86_64-linux-gnu/libhts.a -L=-z
-L=relro -L=-z -L=now -L=-flto -fvisibility=hidden
-L=/usr/lib/x86_64-linux-gnu/libbz2.a -L=/usr/lib/x86_64-linux-gnu/libdeflate.a
-L=-lm -L=-lpthread -L=/usr/lib/x86_64-linux-gnu/liblzma.a
/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/liblz4.so
/usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libcrypto.so
/usr/lib/x86_64-linux-gnu/liblzma.so -L=-rpath
-L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu
-L=-rpath-link -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu
-L=-rpath-link -L=/usr/lib/x86_64-linux-gnu
bgzf.c:415: error: undefined reference to 'compressBound'
collect2: error: ld returned 1 exit status
Error: /usr/bin/cc failed with status: 1
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v
returned exit code 1
I admit I need help here.
Kind regards
Andreas.
--
http://fam-tille.de
