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Error compiling Rust program #76

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mdekstrand opened this issue Mar 12, 2021 · 3 comments
Open
1 task done

Error compiling Rust program #76

mdekstrand opened this issue Mar 12, 2021 · 3 comments

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

@pkgw
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pkgw commented Mar 16, 2021

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.

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