Hi, I’m trying to use a Rust package on baobab2, mkmolinfo. I first installed Rust, following these instructions. Then I did module load GCCcore/8.2.0 OpenSSL/1.1.1b and tried to run Cargo build to compile the package. However, it fails with the error below. I have tried to fix this by installing clang and other ways, but they all failed unfortunately, and nearly all solutions I found require root access. I would be very grateful for any help?
Apologies if this is not the right forum to post this question. The specifics may not be of general interest, although it might be useful for others too if Rust and dependancies were available on baobab via module load.
Many thanks,
Chris
Error:
[rands@login2 mkmolinfo]$ cargo build
Compiling rust-htslib v0.24.0
error: failed to run custom build command for `rust-htslib v0.24.0`
Caused by:
process didn't exit successfully: `/home/rands/MKMOLINFO/mkmolinfo/target/debug/build/rust-htslib-643757b5f95326c9/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 '#define HAVE_LZMA_H 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o kfunc.o kfunc.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o knetfile.o knetfile.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o kstring.o kstring.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o bgzf.o bgzf.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o errmod.o errmod.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o faidx.o faidx.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o hfile.o hfile.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9"' > version.h
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o hts.o hts.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o hts_os.o hts_os.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o md5.o md5.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o multipart.o multipart.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o probaln.o probaln.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o realn.o realn.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o regidx.o regidx.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o sam.o sam.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o vcf_sweep.o vcf_sweep.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o tbx.o tbx.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o textutils.o textutils.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o thread_pool.o thread_pool.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o vcf.o vcf.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o vcfutils.o vcfutils.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o cram/files.o cram/files.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o cram/mFILE.o cram/mFILE.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/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 /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o cram/sam_header.o cram/sam_header.c
cc -ffunction-sections -fdata-sections -fPIC -g -fno-omit-frame-pointer -m64 -static -I /home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include -I. -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.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/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-static" "-I" "/home/rands/MKMOLINFO/mkmolinfo/target/debug/build/bzip2-sys-2c953a1366e86d23/out/include" "-o" "/home/rands/MKMOLINFO/mkmolinfo/target/debug/build/rust-htslib-fccf6082e136540b/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" "/home/rands/MKMOLINFO/mkmolinfo/target/debug/build/rust-htslib-fccf6082e136540b/out/libwrapper.a" "/home/rands/MKMOLINFO/mkmolinfo/target/debug/build/rust-htslib-fccf6082e136540b/out/wrapper.o"
exit code: 0
cargo:rustc-link-lib=static=wrapper
cargo:rustc-link-search=native=/home/rands/MKMOLINFO/mkmolinfo/target/debug/build/rust-htslib-fccf6082e136540b/out
--- stderr
thread 'main' panicked at 'Unable to find libclang: "couldn\'t find any valid shared libraries matching: [\'libclang.so\', \'libclang-*.so\', \'libclang.so.*\'], set the `LIBCLANG_PATH` environment variable to a path where one of these files can be found (invalid: [])"', src/libcore/result.rs:999:5
note: Run with `RUST_BACKTRACE=1` environment variable to display a backtrace.