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conda-forge / rust-feedstock

A conda-smithy repository for rust.
BSD 3-Clause "New" or "Revised" License
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Error compiling Rust program #76

Open mdekstrand opened 3 years ago

mdekstrand commented 3 years ago

Issue:

building a Rust program with Rust from conda-forge fails with linker errors (host OS Red Hat 8):

``` = note: /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-6f77337c1826707d.rlib(std-6f77337c1826707d.std.4qsyoc55-cgu.0.rcgu.o): in function `std::sys::unix::time::inner::now': /rustc/cb75ad5db02783e8b0222fee363c5f63f7e2cf5b//library/std/src/sys/unix/time.rs:371: undefined reference to `clock_gettime' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /rustc/cb75ad5db02783e8b0222fee363c5f63f7e2cf5b//library/std/src/sys/unix/time.rs:371: undefined reference to `clock_gettime' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libdl.so: undefined reference to `_dl_catch_error@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__nanosleep_nocancel@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libdl.so: undefined reference to `_dl_signal_error@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__twalk@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/librt.so: undefined reference to `memcpy@GLIBC_2.14' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__call_tls_dtors@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__tsearch@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__clock_gettime@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__mmap@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__tdelete@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__h_errno@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `_IO_enable_locks@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__mktemp@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/librt.so: undefined reference to `__socket@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__tfind@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__madvise@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__sigtimedwait@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__libc_fcntl64@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__getrlimit@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__pause_nocancel@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__tunable_get_val@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__write_nocancel@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__ctype_init@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__mprotect@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/librt.so: undefined reference to `__libc_pread@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__munmap@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__open64_nocancel@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libpthread.so: undefined reference to `__read_nocancel@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/librt.so: undefined reference to `__close_nocancel@GLIBC_PRIVATE' /home/MICHAELEKSTRAND/anaconda3/envs/bookdata/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/librt.so: undefined reference to `__recv@GLIBC_PRIVATE' collect2: error: ld returned 1 exit status ```


Environment (conda list):

``` $ conda list _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge abseil-cpp 20200923.3 h9c3ff4c_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 20.1.0 py38h497a2fe_2 conda-forge arrow-cpp 3.0.0 py38h6da0e5f_9_cpu conda-forge async_generator 1.10 py_0 conda-forge at-spi2-atk 2.38.0 hdfca744_2 conda-forge at-spi2-core 2.38.0 hdfca744_2 conda-forge atk-1.0 2.36.0 h3371d22_4 conda-forge atpublic 1.0 py_0 conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge aws-c-cal 0.4.5 h76129ab_8 conda-forge aws-c-common 0.5.2 h7f98852_0 conda-forge aws-c-event-stream 0.2.7 h6bac3ce_1 conda-forge aws-c-io 0.9.1 ha5b09cb_1 conda-forge aws-checksums 0.1.11 h99e32c3_3 conda-forge aws-sdk-cpp 1.8.151 hceb1b1e_1 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge binutils 2.35.1 hdd6e379_2 conda-forge binutils_impl_linux-64 2.35.1 h193b22a_2 conda-forge binutils_linux-64 2.35 h67ddf6f_30 conda-forge bleach 3.3.0 pyh44b312d_0 conda-forge boost 1.74.0 py38hc10631b_3 conda-forge boost-cpp 1.74.0 hc6e9bd1_2 conda-forge boto3 1.17.26 pyhd8ed1ab_0 conda-forge botocore 1.20.26 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h9c3ff4c_4 conda-forge brotlipy 0.7.0 py38h497a2fe_1001 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h7f98852_1 conda-forge c-compiler 1.1.3 h7f98852_0 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 h7979940_1007 conda-forge cairomm 1.12.2 ha770c72_3 conda-forge cairomm-1.0 1.12.2 h56b4340_3 conda-forge certifi 2020.12.5 py38h578d9bd_1 conda-forge cffi 1.14.5 py38ha65f79e_0 conda-forge chardet 4.0.0 py38h578d9bd_1 conda-forge chromalog 1.0.5 pypi_0 pypi colorama 0.4.4 pyh9f0ad1d_0 conda-forge commonmark 0.9.1 py_0 conda-forge configobj 5.0.6 py_0 conda-forge cryptography 3.4.6 py38ha5dfef3_0 conda-forge curl 7.75.0 h979ede3_0 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 hfdff14a_1 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge diskcache 5.2.1 pyh44b312d_0 conda-forge distro 1.5.0 pyh9f0ad1d_0 conda-forge docopt 0.6.2 py_1 conda-forge dpath 2.0.1 py38h578d9bd_0 conda-forge dulwich 0.20.20 py38h497a2fe_0 conda-forge dvc 2.0.5 py38h578d9bd_0 conda-forge entrypoints 0.3 pyhd8ed1ab_1003 conda-forge epoxy 1.5.5 h7f98852_0 conda-forge expat 2.2.10 h9c3ff4c_0 conda-forge flatten-dict 0.3.0 pyh9f0ad1d_0 conda-forge flufl.lock 3.2 py_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 2.001 hab24e00_0 conda-forge font-ttf-source-code-pro 2.030 hab24e00_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.13.1 hba837de_1004 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge fsspec 0.8.7 pyhd8ed1ab_0 conda-forge funcy 1.15 pyh9f0ad1d_0 conda-forge future 0.18.2 py38h578d9bd_3 conda-forge gcc_impl_linux-64 9.3.0 h70c0ae5_18 conda-forge gcc_linux-64 9.3.0 hf25ea35_30 conda-forge gdk-pixbuf 2.42.2 h0c95a7a_2 conda-forge gettext 0.19.8.1 h0b5b191_1005 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge giflib 5.2.1 h36c2ea0_2 conda-forge gitdb 4.0.5 pyhd8ed1ab_1 conda-forge gitdb2 4.0.2 py_0 conda-forge gitpython 3.1.14 pyhd8ed1ab_0 conda-forge glib 2.66.7 h9c3ff4c_1 conda-forge glib-tools 2.66.7 h9c3ff4c_1 conda-forge glog 0.4.0 h49b9bf7_3 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gobject-introspection 1.66.1 py38h951ac0e_4 conda-forge grandalf 0.6 py_0 conda-forge graph-tool 2.37 py38h9a62468_1 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge graphviz 2.46.1 h93c640b_4 conda-forge grpc-cpp 1.36.2 h7919d58_0 conda-forge gtk2 2.24.33 hab0c2f8_0 conda-forge gtk3 3.24.26 h2369adc_0 conda-forge gts 0.7.6 h64030ff_2 conda-forge harfbuzz 2.7.4 h5cf4720_0 conda-forge hicolor-icon-theme 0.17 ha770c72_2 conda-forge html5lib 1.1 pyh9f0ad1d_0 conda-forge icu 68.1 h58526e2_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge importlib-metadata 3.7.2 py38h578d9bd_0 conda-forge invoke 1.5.0 pyhd3deb0d_0 conda-forge ipykernel 5.5.0 py38h81c977d_1 conda-forge ipython 7.21.0 py38h81c977d_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge jedi 0.18.0 py38h578d9bd_2 conda-forge jinja2 2.11.3 pyh44b312d_0 conda-forge jmespath 0.10.0 pyh9f0ad1d_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge jsonpath-ng 1.5.2 pyh9f0ad1d_0 conda-forge jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge jupyter_client 6.1.11 pyhd8ed1ab_1 conda-forge jupyter_core 4.7.1 py38h578d9bd_0 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge kiwisolver 1.3.1 py38h1fd1430_1 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge libblas 3.9.0 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libcurl 7.75.0 hc4aaa36_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 hcdb4288_3 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-devel_linux-64 9.3.0 h7864c58_18 conda-forge libgcc-ng 9.3.0 h2828fa1_18 conda-forge libgd 2.3.0 h47910db_1 conda-forge libgfortran-ng 9.3.0 hff62375_18 conda-forge libgfortran5 9.3.0 hff62375_18 conda-forge libgit2 1.1.0 h3974521_1 conda-forge libglib 2.66.7 h3e27bee_1 conda-forge libgomp 9.3.0 h2828fa1_18 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 8_openblas conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libopenblas 0.3.12 pthreads_h4812303_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libpq 13.1 hfd2b0eb_2 conda-forge libprotobuf 3.15.6 h780b84a_0 conda-forge librsvg 2.50.3 hfa39831_1 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libssh2 1.9.0 ha56f1ee_6 conda-forge libstdcxx-ng 9.3.0 h6de172a_18 conda-forge libthrift 0.14.1 he6d91bd_1 conda-forge libtiff 4.2.0 hdc55705_0 conda-forge libtool 2.4.6 h58526e2_1007 conda-forge libutf8proc 2.6.1 h7f98852_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp 1.2.0 h3452ae3_0 conda-forge libwebp-base 1.2.0 h7f98852_0 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxml2 2.9.10 h72842e0_3 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 1.1.1 py38h497a2fe_3 conda-forge matplotlib-base 3.3.4 py38h0efea84_0 conda-forge mistune 0.8.4 py38h497a2fe_1003 conda-forge more-itertools 8.7.0 pyhd8ed1ab_0 conda-forge nanotime 0.5.2 py_0 conda-forge natural 0.2.0 pypi_0 pypi nbclient 0.5.3 pyhd8ed1ab_0 conda-forge nbconvert 6.0.7 py38h578d9bd_3 conda-forge nbformat 5.1.2 pyhd8ed1ab_1 conda-forge ncurses 6.2 h58526e2_4 conda-forge nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge networkx 2.5 py_0 conda-forge notebook 6.2.0 py38h578d9bd_0 conda-forge numpy 1.20.1 py38h18fd61f_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openssl 1.1.1j h7f98852_0 conda-forge orc 1.6.7 heec2584_1 conda-forge packaging 20.9 pyh44b312d_0 conda-forge pandas 1.2.3 py38h51da96c_0 conda-forge pandoc 2.12 h7f98852_0 conda-forge pandocfilters 1.4.2 py_1 conda-forge pango 1.42.4 h69149e4_5 conda-forge parquet-cpp 1.5.1 2 conda-forge parso 0.8.1 pyhd8ed1ab_0 conda-forge pathlib2 2.3.5 py38h578d9bd_3 conda-forge pathspec 0.8.1 pyhd3deb0d_0 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge pcre2 10.36 h032f7d1_1 conda-forge pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.1.2 py38ha0e1e83_0 conda-forge pip 21.0.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge ply 3.11 py_1 conda-forge postgresql 13.1 h6303168_2 conda-forge prometheus_client 0.9.0 pyhd3deb0d_0 conda-forge prompt-toolkit 3.0.17 pyha770c72_0 conda-forge psutil 5.8.0 py38h497a2fe_1 conda-forge psycopg2 2.8.6 py38h497a2fe_2 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pyarrow 3.0.0 py38h92f0514_9_cpu conda-forge pyasn1 0.4.8 py_0 conda-forge pycairo 1.20.0 py38h323dad1_1 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pydot 1.4.2 py38h578d9bd_0 conda-forge pygit2 1.5.0 py38h497a2fe_0 conda-forge pygments 2.8.1 pyhd8ed1ab_0 conda-forge pygobject 3.38.0 py38h073a499_4 conda-forge pygtrie 2.3.2 pyh8c360ce_0 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyrsistent 0.17.3 py38h497a2fe_2 conda-forge pysocks 1.7.1 py38h578d9bd_3 conda-forge python 3.8.8 hffdb5ce_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.8 1_cp38 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyzmq 22.0.3 py38h2035c66_1 conda-forge re2 2020.11.01 h58526e2_0 conda-forge readline 8.0 he28a2e2_2 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge rich 9.13.0 py38h578d9bd_0 conda-forge ruamel.yaml 0.16.12 py38h497a2fe_2 conda-forge ruamel.yaml.clib 0.2.2 py38h497a2fe_2 conda-forge rust 1.50.0 h3bf0571_0 conda-forge rust-std-x86_64-unknown-linux-gnu 1.50.0 hc1431ca_0 conda-forge s2n 1.0.0 h9b69904_0 conda-forge s3transfer 0.3.4 pyhd8ed1ab_0 conda-forge scipy 1.6.0 py38hb2138dd_0 conda-forge seaborn 0.11.1 hd8ed1ab_1 conda-forge seaborn-base 0.11.1 pyhd8ed1ab_1 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py38h578d9bd_3 conda-forge setuptools-scm 5.0.2 pyh44b312d_0 conda-forge setuptools_scm 5.0.2 hd8ed1ab_0 conda-forge shortuuid 1.0.1 py38h578d9bd_4 conda-forge shtab 1.3.5 pyh44b312d_0 conda-forge sigcpp-2.0 2.10.3 h58526e2_0 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge smmap 3.0.5 pyh44b312d_0 conda-forge snappy 1.1.8 he1b5a44_3 conda-forge sparsehash 2.0.3 hf484d3e_1000 conda-forge sqlalchemy 1.3.23 py38h497a2fe_0 conda-forge sqlite 3.34.0 h74cdb3f_0 conda-forge sqlparse 0.4.1 pyh9f0ad1d_0 conda-forge statsmodels 0.12.2 py38h5c078b8_0 conda-forge sysroot_linux-64 2.12 h77966d4_13 conda-forge tabulate 0.8.9 pyhd8ed1ab_0 conda-forge terminado 0.9.2 py38h578d9bd_0 conda-forge testpath 0.4.4 py_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tornado 6.1 py38h497a2fe_1 conda-forge tqdm 4.59.0 pyhd8ed1ab_0 conda-forge traitlets 5.0.5 py_0 conda-forge typing_extensions 3.7.4.3 py_0 conda-forge tzcode 2021a h7f98852_1 conda-forge tzdata 2021a he74cb21_0 conda-forge urllib3 1.26.3 pyhd8ed1ab_0 conda-forge voluptuous 0.12.1 pyhd3deb0d_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge widgetsnbextension 3.5.1 py38h578d9bd_4 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.0 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge zc.lockfile 2.0 py_0 conda-forge zeromq 4.3.4 h9c3ff4c_0 conda-forge zipp 3.4.1 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstandard 0.15.2 py38h497a2fe_0 conda-forge zstd 1.4.9 ha95c52a_0 conda-forge ```


Details about conda and system ( conda info ):

``` $ conda info active environment : bookdata active env location : /home/MICHAELEKSTRAND/anaconda3/envs/bookdata shell level : 1 user config file : /home/MICHAELEKSTRAND/.condarc populated config files : /home/MICHAELEKSTRAND/.condarc conda version : 4.8.2 conda-build version : 3.18.11 python version : 3.7.6.final.0 virtual packages : __glibc=2.28 base environment : /home/MICHAELEKSTRAND/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/MICHAELEKSTRAND/anaconda3/pkgs /home/MICHAELEKSTRAND/.conda/pkgs envs directories : /home/MICHAELEKSTRAND/anaconda3/envs /home/MICHAELEKSTRAND/.conda/envs platform : linux-64 user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.6 Linux/4.18.0-193.28.1.el8_2.x86_64 rhel/8.3 glibc/2.28 UID:GID : 412577:412577 netrc file : /home/MICHAELEKSTRAND/.netrc offline mode : False ```
mdekstrand commented 3 years ago

I can work around this error by setting the environment variable:

RUSTFLAGS="-L native=$CONDA_BUILD_SYSROOT/usr/lib64 -L native=$CONDA_BUILD_SYSROOT/lib64"
jakirkham commented 3 years ago

Yeah it sounds like Rust isn't respecting the compiler's sysroot. Not sure why that is (not a Rust expert)

pkgw commented 3 years ago

Might be related to #71? I'd have thought that if rustc was invoking the right toolchain programs, which it seems to be, it wouldn't be necessary to add any extra magic arguments to the command lines, but it seems that at least sometimes we need to do something more here.