Build fails with conda

[Hoeze]

Reproducer:

git clone https://github.com/NKI-GCF/gensum
cd gensum
conda install rust
cargo build --release

Result:

   Compiling gensum v0.1.0 (/home/<user>/Projects/gensum)
error: linking with `/opt/anaconda/envs/rust/bin/x86_64-conda-linux-gnu-cc` failed: exit status: 1
  |
  = note: "/opt/anaconda/envs/rust/bin/x86_64-conda-linux-gnu-cc" "-m64" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.0.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.1.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.10.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.11.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.2.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.3.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.4.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.5.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.6.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.7.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.8.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.gensum.6b8eeb36-cgu.9.rcgu.o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699.3ai763jtq5v65lqf.rcgu.o" "-Wl,--as-needed" "-L" "/home/<user>/Projects/gensum/target/release/deps" "-L" "/usr/lib" "-L" "/home/<user>/Projects/gensum/target/release/build/lzma-sys-82d560a9ec2a96e8/out" "-L" "/home/<user>/Projects/gensum/target/release/build/hts-sys-63c9e5a7389b1df2/out" "-L" "/home/<user>/Projects/gensum/target/release/build/curl-sys-a3e5f0f83674a732/out/build" "-L" "/home/<user>/Projects/gensum/target/release/build/libz-sys-26887ec18a5d8ff4/out/lib" "-L" "/home/<user>/Projects/gensum/target/release/build/libz-sys-26887ec18a5d8ff4/out/lib" "-L" "/home/<user>/Projects/gensum/target/release/build/openssl-sys-548701f82ae0d3f1/out/openssl-build/install/lib" "-L" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/home/<user>/Projects/gensum/target/release/deps/libniffler-56b4c6949e42dd44.rlib" "/home/<user>/Projects/gensum/target/release/deps/libxz2-23eaeb3809d709b9.rlib" "/home/<user>/Projects/gensum/target/release/deps/libbzip2-60f74516ee42d617.rlib" "/home/<user>/Projects/gensum/target/release/deps/libflate2-d09d8813daf84f72.rlib" "/home/<user>/Projects/gensum/target/release/deps/libminiz_oxide-d16dbb21614b649d.rlib" "/home/<user>/Projects/gensum/target/release/deps/libadler-e75f7594b8bae6be.rlib" "/home/<user>/Projects/gensum/target/release/deps/libcrc32fast-7ccf8c75e49749e3.rlib" "/home/<user>/Projects/gensum/target/release/deps/libenum_primitive-e09ea9aedc1a7c7e.rlib" "/home/<user>/Projects/gensum/target/release/deps/libnum_traits-8c682da58e2af5a8.rlib" "/home/<user>/Projects/gensum/target/release/deps/libcfg_if-f6a35cef654aa08d.rlib" "/home/<user>/Projects/gensum/target/release/deps/librust_htslib-1cff1a0d1341cc83.rlib" "/home/<user>/Projects/gensum/target/release/deps/libhts_sys-7e8095ab54e350ce.rlib" "/home/<user>/Projects/gensum/target/release/deps/libcurl_sys-60dba45bb7001c8f.rlib" "/home/<user>/Projects/gensum/target/release/deps/libopenssl_sys-6c280da2e4e7a01f.rlib" "/home/<user>/Projects/gensum/target/release/deps/liblzma_sys-abebe815e7a84592.rlib" "/home/<user>/Projects/gensum/target/release/deps/libbzip2_sys-6e191dbb478ea6a7.rlib" "/home/<user>/Projects/gensum/target/release/deps/liblibz_sys-cdd411373bbfb160.rlib" "/home/<user>/Projects/gensum/target/release/deps/libieee754-2e2a7a919f0748a3.rlib" "/home/<user>/Projects/gensum/target/release/deps/liburl-3b4f4ed37665a91b.rlib" "/home/<user>/Projects/gensum/target/release/deps/libidna-80163f900f3ff87b.rlib" "/home/<user>/Projects/gensum/target/release/deps/libunicode_normalization-b6e358d7e2d8421a.rlib" "/home/<user>/Projects/gensum/target/release/deps/libtinyvec-a8db09191bb25ded.rlib" "/home/<user>/Projects/gensum/target/release/deps/libtinyvec_macros-9e6dc58399d26886.rlib" "/home/<user>/Projects/gensum/target/release/deps/libunicode_bidi-ea0b37ba75857135.rlib" "/home/<user>/Projects/gensum/target/release/deps/libform_urlencoded-e5a8cba9af4c5455.rlib" "/home/<user>/Projects/gensum/target/release/deps/libpercent_encoding-39102524c2d994d3.rlib" "/home/<user>/Projects/gensum/target/release/deps/libmatches-9acb7d43912c29d5.rlib" "/home/<user>/Projects/gensum/target/release/deps/libbio_types-bd05a42c2a333733.rlib" "/home/<user>/Projects/gensum/target/release/deps/libthiserror-5de8223321bf1013.rlib" "/home/<user>/Projects/gensum/target/release/deps/libregex-9d2985763a1f01a7.rlib" "/home/<user>/Projects/gensum/target/release/deps/libregex_syntax-a29410a23c86ff7a.rlib" "/home/<user>/Projects/gensum/target/release/deps/libaho_corasick-9fbfb3e032d00e77.rlib" "/home/<user>/Projects/gensum/target/release/deps/libmemchr-9fec3276a4abc327.rlib" "/home/<user>/Projects/gensum/target/release/deps/liblinear_map-27241d64e4177a59.rlib" "/home/<user>/Projects/gensum/target/release/deps/liblazy_static-fe3ffb0d817d13d7.rlib" "/home/<user>/Projects/gensum/target/release/deps/libnewtype_derive-947572ba6887247a.rlib" "/home/<user>/Projects/gensum/target/release/deps/libcustom_derive-206c5fd94b81fee1.rlib" "/home/<user>/Projects/gensum/target/release/deps/libnclist-c29a058fa2326627.rlib" "/home/<user>/Projects/gensum/target/release/deps/libitertools-355bbf4b5a1e746a.rlib" "/home/<user>/Projects/gensum/target/release/deps/libeither-08f90d3f0d88bbf0.rlib" "/home/<user>/Projects/gensum/target/release/deps/libitoa-875eff8244583b39.rlib" "/home/<user>/Projects/gensum/target/release/deps/libindexmap-5d941a2530ae39d6.rlib" "/home/<user>/Projects/gensum/target/release/deps/libhashbrown-1740255a0c675020.rlib" "/home/<user>/Projects/gensum/target/release/deps/libatoi-5c352f89951263c5.rlib" "/home/<user>/Projects/gensum/target/release/deps/libnum_traits-190c641f9b28952f.rlib" "/home/<user>/Projects/gensum/target/release/deps/libanyhow-07dc354720abd4cf.rlib" "/home/<user>/Projects/gensum/target/release/deps/libclap-6f873020885f692e.rlib" "/home/<user>/Projects/gensum/target/release/deps/libvec_map-42adc355362c5416.rlib" "/home/<user>/Projects/gensum/target/release/deps/libtextwrap-b39d0db27731a433.rlib" "/home/<user>/Projects/gensum/target/release/deps/libunicode_width-3bf99c6b4d3f3e20.rlib" "/home/<user>/Projects/gensum/target/release/deps/libstrsim-cd375033641a485f.rlib" "/home/<user>/Projects/gensum/target/release/deps/libbitflags-4208964463941641.rlib" "/home/<user>/Projects/gensum/target/release/deps/libatty-8aad9bacf4c0a634.rlib" "/home/<user>/Projects/gensum/target/release/deps/liblibc-de5a67a0b94dcbd6.rlib" "/home/<user>/Projects/gensum/target/release/deps/libansi_term-1396373762392330.rlib" "-Wl,--start-group" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-008055cc7d873802.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-06f01ac2578bda94.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-f9a3c3274a1835e0.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-d4cbb754ee9f4daa.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-95c14e1c1e3ebcc4.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-d489f0ca872880cc.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-75f07df0b18fea39.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd_detect-0c35b278736219a2.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-e530649c9a06e3c6.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-6b148909d375a785.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-cd15fa647f4775d1.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-74be3a703f788ba2.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-8f2c5b445c28b2e3.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-8480e85e0be96197.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-ac23a75f6f42004e.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-557ba8776e04d182.rlib" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-4beb03d03503c439.rlib" "-Wl,--end-group" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-dd7db1bec6909f24.rlib" "-Wl,-Bdynamic" "-lbz2" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-Wl,--eh-frame-hdr" "-Wl,-znoexecstack" "-L" "/opt/anaconda/envs/rust/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "/home/<user>/Projects/gensum/target/release/deps/gensum-314a923d97f3b699" "-Wl,--gc-sections" "-pie" "-Wl,-zrelro" "-Wl,-znow" "-Wl,-O1" "-nodefaultlibs"
  = note: /opt/anaconda/envs/rust/bin/../lib/gcc/x86_64-conda-linux-gnu/11.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/<user>/Projects/gensum/target/release/deps/libopenssl_sys-6c280da2e4e7a01f.rlib(threads_pthread.o): in function `fork_once_func':
          threads_pthread.c:(.text.fork_once_func+0x16): undefined reference to `pthread_atfork'
          collect2: error: ld returned 1 exit status
          
  = help: some `extern` functions couldn't be found; some native libraries may need to be installed or have their path specified
  = note: use the `-l` flag to specify native libraries to link
  = note: use the `cargo:rustc-link-lib` directive to specify the native libraries to link with Cargo (see https://doc.rust-lang.org/cargo/reference/build-scripts.html#cargorustc-link-libkindname)

error: could not compile `gensum` due to previous error

[veldsla]

I can reproduce this with a conda rust environmnent. The problem is triggered more upstream because any basic rust-htslib fails to build. It's probably even more upstream somewhere in the openssl/openssl-sys crate. Conda's linker fails to find the required library and I haven't been able to fix that.

It is however more common to install rust using rustup. This works without issues for me.
Maybe the rust-htslib people are interested in picking this up because they probably also use conda.