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rust-bio / rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
MIT License
308 stars 80 forks source link

libclang on centos7 is giving me issues #200

Closed lskatz closed 4 years ago

lskatz commented 4 years ago 
[gzu2@monolith3 any2bed]$ grep -i ^bio Cargo.toml
bio         = {version = "0.30", default-features=false}
[gzu2@monolith3 any2bed]$ cargo build
   Compiling hts-sys v1.10.2
error: failed to run custom build command for `hts-sys v1.10.2`

Caused by:
  process didn't exit successfully: `/scicomp/home/gzu2/src/any2bed/target/debug/build/hts-sys-cb6cc6623325f2ff/build-script-build` (exit code: 101)
--- stdout
OPT_LEVEL = Some("0")
TARGET = Some("x86_64-unknown-linux-gnu")
HOST = Some("x86_64-unknown-linux-gnu")
CC_x86_64-unknown-linux-gnu = None
CC_x86_64_unknown_linux_gnu = None
HOST_CC = None
CC = None
CFLAGS_x86_64-unknown-linux-gnu = None
CFLAGS_x86_64_unknown_linux_gnu = None
HOST_CFLAGS = None
CFLAGS = None
CRATE_CC_NO_DEFAULTS = None
DEBUG = Some("true")
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#ifndef __APPLE__' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o kfunc.o kfunc.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o knetfile.o knetfile.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o kstring.o kstring.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o bgzf.o bgzf.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o errmod.o errmod.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o faidx.o faidx.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o header.o header.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o hfile.o hfile.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION_TEXT "1.10.2"' > version.h
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o hts.o hts.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o hts_os.o hts_os.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o md5.o md5.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o multipart.o multipart.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o probaln.o probaln.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o realn.o realn.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o regidx.o regidx.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o region.o region.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o sam.o sam.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o vcf_sweep.o vcf_sweep.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o tbx.o tbx.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o textutils.o textutils.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o thread_pool.o thread_pool.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o vcf.o vcf.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o vcfutils.o vcfutils.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_decode.o cram/cram_decode.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_encode.o cram/cram_encode.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_external.o cram/cram_external.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_index.o cram/cram_index.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_io.o cram/cram_io.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/cram_stats.o cram/cram_stats.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/mFILE.o cram/mFILE.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/rANS_static.o cram/rANS_static.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o cram/string_alloc.o cram/string_alloc.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include -I /usr/include -I.  -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o
ranlib libhts.a
running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-static" "-I" "/scicomp/home/gzu2/src/any2bed/target/debug/build/bzip2-sys-6298d5f5b6c57b2e/out/include" "-I" "/usr/include" "-o" "/scicomp/home/gzu2/src/any2bed/target/debug/build/hts-sys-2b88fa015e6168f7/out/wrapper.o" "-c" "wrapper.c"
exit code: 0
AR_x86_64-unknown-linux-gnu = None
AR_x86_64_unknown_linux_gnu = None
HOST_AR = None
AR = None
running: "ar" "crs" "/scicomp/home/gzu2/src/any2bed/target/debug/build/hts-sys-2b88fa015e6168f7/out/libwrapper.a" "/scicomp/home/gzu2/src/any2bed/target/debug/build/hts-sys-2b88fa015e6168f7/out/wrapper.o"
exit code: 0
cargo:rustc-link-lib=static=wrapper
cargo:rustc-link-search=native=/scicomp/home/gzu2/src/any2bed/target/debug/build/hts-sys-2b88fa015e6168f7/out

--- stderr
thread 'main' panicked at 'Unable to find libclang: "the `libclang` shared library at /usr/lib64/clang-private/libclang.so.7 could not be opened: libclangAST.so.7: cannot open shared object file: No such file or directory"', src/libcore/result.rs:999:5
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace.
[gzu2@monolith3 any2bed]$ ls -lh /usr/lib64/clang-private/libclang.so.7
-rwxr-xr-x. 1 root root 546K Aug  8  2019 /usr/lib64/clang-private/libclang.so.7*
lskatz commented 4 years ago

fixed with

[gzu2@monolith3 any2bed]$ export PKG_CONFIG_PATH=/lib64/pkgconfig
[gzu2@monolith3 any2bed]$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/clang-private