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conda-forge / readline-feedstock

A conda-smithy repository for readline.
BSD 3-Clause "New" or "Revised" License
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libreadline.so.8: undefined symbol: tputs #24

Open nick-youngblut opened 2 years ago

nick-youngblut commented 2 years ago

error

conda-forge::readlilne=8.1.2 generates the following error when calling R (conda-forge::r-base):

/ebio/abt3_projects/temp_data/nyoungblut/tmp/envs/tidyverse/lib/R/bin/exec/R: symbol lookup error: /ebio/abt3_projects/temp_data/nyoungblut/tmp/envs/tidyverse/lib/R/bin/exec/../../lib/../../libreadline.so.8: undefined symbol: tputs

This error seems to occur regardless of the R version.

Changing to conda-forge::readlilne=8.1.0 resolves the issue.

conda list

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h6acc77f_1    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_4    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.26           h06a4308_2
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
cffi                      1.15.0          py310h0fdd8cc_0    conda-forge
curl                      7.81.0               h2574ce0_0    conda-forge
dbus                      1.13.18              hb2f20db_0
debugpy                   1.5.1           py310h122e73d_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.3             pyhd8ed1ab_1003    conda-forge
expat                     2.4.2                h9c3ff4c_0    conda-forge
flit-core                 3.6.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.11.0               h70c0345_0
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc_impl_linux-64         9.4.0               h03d3576_11    conda-forge
gcc_linux-64              9.4.0                h391b98a_4    conda-forge
gettext                   0.21.0               hf68c758_0
gfortran_impl_linux-64    9.4.0               h0003116_11    conda-forge
gfortran_linux-64         9.4.0                hf0ab688_4    conda-forge
glib                      2.70.2               h780b84a_1    conda-forge
glib-tools                2.70.2               h780b84a_1    conda-forge
graphite2                 1.3.14               h23475e2_0
gsl                       2.7                  he838d99_0    conda-forge
gst-plugins-base          1.18.5               hf529b03_2    conda-forge
gstreamer                 1.18.5               h9f60fe5_3    conda-forge
gxx_impl_linux-64         9.4.0               h03d3576_11    conda-forge
gxx_linux-64              9.4.0                h0316aca_4    conda-forge
harfbuzz                  3.1.1                h83ec7ef_0    conda-forge
icu                       68.2                 h9c3ff4c_0    conda-forge
importlib-metadata        4.10.0          py310hff52083_0    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.6.1           py310hfdc917e_0    conda-forge
ipython                   7.31.0          py310hff52083_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.1          py310hff52083_0    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
jsonschema                4.3.3              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0           py310hff52083_7    conda-forge
jupyter_client            7.1.0              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.1           py310hff52083_1    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
krb5                      1.19.2               hcc1bbae_3    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           12_linux64_openblas    conda-forge
libcblas                  3.9.0           12_linux64_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcurl                   7.81.0               h2574ce0_0    conda-forge
libdeflate                1.8                  h7f98852_0    conda-forge
libedit                   3.1.20210714         h7f8727e_0
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     9.4.0               hd854feb_11    conda-forge
libgcc-ng                 11.2.0              h1d223b6_11    conda-forge
libgfortran-ng            11.2.0              h69a702a_11    conda-forge
libgfortran5              11.2.0              h5c6108e_11    conda-forge
libglib                   2.70.2               h174f98d_1    conda-forge
libgomp                   11.2.0              h1d223b6_11    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           12_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnghttp2                1.46.0               hce63b2e_0
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.5                h27cfd23_1
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     13.5                 hd57d9b9_1    conda-forge
libsanitizer              9.4.0               h79bfe98_11    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-devel_linux-64  9.4.0               hd854feb_11    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libtiff                   4.3.0                h6f004c6_2    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.14                 h7b6447c_0
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
markupsafe                2.0.1           py310h6acc77f_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py310h6acc77f_1005    conda-forge
mysql-common              8.0.27               ha770c72_3    conda-forge
mysql-libs                8.0.27               hfa10184_3    conda-forge
nb_conda_kernels          2.3.1           py310hff52083_1    conda-forge
nbclient                  0.5.9              pyhd8ed1ab_0    conda-forge
nbconvert                 6.4.0           py310hff52083_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
notebook                  6.4.6              pyha770c72_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.74                 hb5efdd6_0    conda-forge
openssl                   1.1.1m               h7f8727e_0
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandoc                    2.16.2               h7f98852_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.48.10              h54213e6_2    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
prometheus_client         0.12.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.24             pyha770c72_0    conda-forge
prompt_toolkit            3.0.24               hd8ed1ab_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.6              pyhd8ed1ab_0    conda-forge
pyqt                      5.12.3          py310hff52083_8    conda-forge
pyqt-impl                 5.12.3          py310h1f8e252_8    conda-forge
pyqt5-sip                 4.19.18         py310h122e73d_8    conda-forge
pyqtchart                 5.12            py310hfcd6d55_8    conda-forge
pyqtwebengine             5.12.1          py310hfcd6d55_8    conda-forge
pyrsistent                0.18.0          py310h6acc77f_0    conda-forge
python                    3.10.1          h62f1059_2_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pyzmq                     22.3.0          py310h675a958_1    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
qtconsole                 5.2.2              pyhd8ed1ab_1    conda-forge
qtconsole-base            5.2.2              pyhd8ed1ab_1    conda-forge
qtpy                      2.0.0              pyhd8ed1ab_0    conda-forge
r-assertthat              0.2.1             r41hc72bb7e_2    conda-forge
r-backports               1.4.1             r41hcfec24a_0    conda-forge
r-base                    4.1.1                hb93adac_1    conda-forge
r-base64enc               0.1_3           r41hcfec24a_1004    conda-forge
r-bit                     4.0.4             r41hcfec24a_0    conda-forge
r-bit64                   4.0.5             r41hcfec24a_0    conda-forge
r-brio                    1.1.3             r41hcfec24a_0    conda-forge
r-callr                   3.7.0             r41hc72bb7e_0    conda-forge
r-cli                     3.1.0             r41h03ef668_0    conda-forge
r-clustermq               0.8.95.2          r41h42bf92c_0    conda-forge
r-colorspace              2.0_2             r41hcfec24a_0    conda-forge
r-crayon                  1.4.2             r41hc72bb7e_0    conda-forge
r-data.table              1.14.2            r41hcfec24a_0    conda-forge
r-desc                    1.4.0             r41hc72bb7e_0    conda-forge
r-diffobj                 0.3.5             r41hcfec24a_0    conda-forge
r-digest                  0.6.29            r41h03ef668_0    conda-forge
r-dplyr                   1.0.7             r41h03ef668_0    conda-forge
r-ellipsis                0.3.2             r41hcfec24a_0    conda-forge
r-evaluate                0.14              r41hc72bb7e_2    conda-forge
r-fansi                   1.0.0             r41hcfec24a_0    conda-forge
r-farver                  2.1.0             r41h03ef668_0    conda-forge
r-fastmap                 1.1.0             r41h03ef668_0    conda-forge
r-generics                0.1.1             r41hc72bb7e_0    conda-forge
r-ggplot2                 3.3.5             r41hc72bb7e_0    conda-forge
r-glue                    1.6.0             r41hcfec24a_0    conda-forge
r-gtable                  0.3.0             r41hc72bb7e_3    conda-forge
r-hms                     1.1.1             r41hc72bb7e_0    conda-forge
r-htmltools               0.5.2             r41h03ef668_0    conda-forge
r-irdisplay               1.1               r41hd8ed1ab_0    conda-forge
r-irkernel                1.3               r41hc72bb7e_0    conda-forge
r-isoband                 0.2.5             r41h03ef668_0    conda-forge
r-jsonlite                1.7.2             r41hcfec24a_0    conda-forge
r-labeling                0.4.2             r41hc72bb7e_1    conda-forge
r-lattice                 0.20_45           r41hcfec24a_0    conda-forge
r-lifecycle               1.0.1             r41hc72bb7e_0    conda-forge
r-magrittr                2.0.1             r41hcfec24a_1    conda-forge
r-mass                    7.3_54            r41hcfec24a_0    conda-forge
r-matrix                  1.4_0             r41he454529_0    conda-forge
r-mgcv                    1.8_38            r41he454529_0    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1004    conda-forge
r-narray                  0.4.1.1           r41hc72bb7e_0    conda-forge
r-nlme                    3.1_153           r41h859d828_0    conda-forge
r-pbdzmq                  0.3_6             r41h42bf92c_0    conda-forge
r-pillar                  1.6.4             r41hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_1    conda-forge
r-pkgload                 1.2.4             r41h03ef668_0    conda-forge
r-plyr                    1.8.6             r41h03ef668_1    conda-forge
r-praise                  1.0.0           r41hc72bb7e_1005    conda-forge
r-prettyunits             1.1.1             r41hc72bb7e_1    conda-forge
r-processx                3.5.2             r41hcfec24a_0    conda-forge
r-progress                1.2.2             r41hc72bb7e_2    conda-forge
r-ps                      1.6.0             r41hcfec24a_0    conda-forge
r-purrr                   0.3.4             r41hcfec24a_1    conda-forge
r-qs                      0.25.2            r41h2d4f71f_0    conda-forge
r-r.methodss3             1.8.1             r41hc72bb7e_0    conda-forge
r-r.oo                    1.24.0            r41hc72bb7e_0    conda-forge
r-r.utils                 2.11.0            r41hc72bb7e_0    conda-forge
r-r6                      2.5.1             r41hc72bb7e_0    conda-forge
r-rapiserialize           0.1.0             r41h03ef668_1    conda-forge
r-rcolorbrewer            1.1_2           r41h785f33e_1003    conda-forge
r-rcpp                    1.0.7             r41h03ef668_0    conda-forge
r-rcppparallel            5.1.5             r41h03ef668_0    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_1    conda-forge
r-renv                    0.15.0            r41hc72bb7e_0    conda-forge
r-repr                    1.1.4             r41h785f33e_0    conda-forge
r-rhpcblasctl             0.21_247.1        r41hcfec24a_0    conda-forge
r-rlang                   0.4.12            r41hcfec24a_0    conda-forge
r-rprojroot               2.0.2             r41hc72bb7e_0    conda-forge
r-rstudioapi              0.13              r41hc72bb7e_0    conda-forge
r-scales                  1.1.1             r41hc72bb7e_0    conda-forge
r-stringfish              0.15.5            r41h03ef668_0    conda-forge
r-stringi                 1.7.6             r41hcabe038_0    conda-forge
r-stringr                 1.4.0             r41hc72bb7e_2    conda-forge
r-testthat                3.1.1             r41h03ef668_0    conda-forge
r-tibble                  3.1.6             r41hcfec24a_0    conda-forge
r-tidyr                   1.1.4             r41h03ef668_0    conda-forge
r-tidyselect              1.1.1             r41hc72bb7e_0    conda-forge
r-tidytable               0.6.6             r41hc72bb7e_0    conda-forge
r-utf8                    1.2.2             r41hcfec24a_0    conda-forge
r-uuid                    1.0_3             r41hcfec24a_0    conda-forge
r-vctrs                   0.3.8             r41hcfec24a_1    conda-forge
r-viridislite             0.4.0             r41hc72bb7e_0    conda-forge
r-waldo                   0.3.1             r41hc72bb7e_0    conda-forge
r-withr                   2.4.3             r41hc72bb7e_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                60.5.0          py310hff52083_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.37.0               h9cd32fc_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
terminado                 0.12.1          py310hff52083_1    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
tornado                   6.1             py310h6acc77f_2    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.5.2           py310hff52083_1    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               1.7.2                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    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
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.7.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.1                ha95c52a_0    conda-forge

conda info

    active environment : /ebio/abt3_projects/temp_data/nyoungblut/tmp/envs/tidyverse
    active env location : /ebio/abt3_projects/temp_data/nyoungblut/tmp/envs/tidyverse
            shell level : 2
       user config file : /ebio/abt3/nyoungblut/.condarc
 populated config files : /ebio/abt3_projects/software/miniconda3/.condarc
                          /ebio/abt3/nyoungblut/.condarc
          conda version : 4.11.0
    conda-build version : not installed
         python version : 3.8.3.final.0
       virtual packages : __linux=5.4.89=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /ebio/abt3_projects/software/miniconda3  (writable)
      conda av data dir : /ebio/abt3_projects/software/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          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
                          https://conda.anaconda.org/leylabmpi/linux-64
                          https://conda.anaconda.org/leylabmpi/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://conda.anaconda.org/qiime2/linux-64
                          https://conda.anaconda.org/qiime2/noarch
          package cache : /ebio/abt3_projects/temp_data/nyoungblut/conda_cache
                          /ebio/abt3/nyoungblut/.conda/pkgs
                          /ebio/abt3_projects/software/miniconda3/pkgs
       envs directories : /ebio/abt3_projects/software/miniconda3/envs
                          /ebio/abt3/nyoungblut/.conda/envs
               platform : linux-64
             user-agent : conda/4.11.0 requests/2.26.0 CPython/3.8.3 Linux/5.4.89 ubuntu/18.04.6 glibc/2.27
                UID:GID : 6354:350
             netrc file : None
           offline mode : False
jakirkham commented 2 years ago

At least according to this SO answer, r-base probably should be linking against ncurses libraries in addition to readline as this symbol comes from ncurses