GMT.jl is broken on Binder

[joa-quim]

I've seen this error when building GMT on Ubuntu latest for CI. I'm guessing the usual dependencies shit between glib and GDAL. My solution wast to use a Ubuntu 2018

[seisman]

But we can't control the Ubuntu version we're using on Binder...

[joa-quim]

There is nothing Julia specific in this error. It should be a problem for PyGMT and GMT Binder sets. Don't you see it?

[seisman]

Yes, the same problem. Something wrong with conda-forge's packages.

[weiji14]

Seems to be still a problem, is this related to https://forum.generic-mapping-tools.org/t/conda-gmt-build-is-unusable-in-julia-windows or separate? Will bumping to Julia v1.6 help (xref JuliaLang/julia#34276 (comment))?

┌ Info: Precompiling GMT [5752ebe1-31b9-557e-87aa-f909b540aa54]
└ @ Base loading.jl:1278
ERROR: LoadError: LoadError: could not load library "/srv/conda/envs/notebook/lib/libgmt.so"
/srv/julia/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /srv/conda/envs/notebook/lib/././libtiledb.so.2.2)
Stacktrace:
 [1] GMT_Create_Session at /srv/julia/pkg/packages/GMT/wprG1/src/libgmt.jl:26 [inlined] (repeats 2 times)
 [2] top-level scope at /srv/julia/pkg/packages/GMT/wprG1/src/get_enums.jl:7
 [3] include(::Function, ::Module, ::String) at ./Base.jl:380
 [4] include at ./Base.jl:368 [inlined]
 [5] include(::String) at /srv/julia/pkg/packages/GMT/wprG1/src/GMT.jl:1
 [6] top-level scope at /srv/julia/pkg/packages/GMT/wprG1/src/GMT.jl:193
 [7] include(::Function, ::Module, ::String) at ./Base.jl:380
 [8] include(::Module, ::String) at ./Base.jl:368
 [9] top-level scope at none:2
 [10] eval at ./boot.jl:331 [inlined]
 [11] eval(::Expr) at ./client.jl:467
 [12] top-level scope at ./none:3
in expression starting at /srv/julia/pkg/packages/GMT/wprG1/src/get_enums.jl:7
in expression starting at /srv/julia/pkg/packages/GMT/wprG1/src/GMT.jl:192

Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to /srv/julia/pkg/compiled/v1.5/GMT/EoU0j_qQLi1.ji.

Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923
 [6] include_string(::Function, ::Module, ::String, ::String) at ./loading.jl:1091

This is the output from conda list. Perhaps we can pin some dependency to a lower version so that GMT.jl will work?

# packages in environment at /srv/conda/envs/notebook:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
alembic                   1.4.2              pyh9f0ad1d_0    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
anyio                     3.1.0            py39hf3d152e_0    conda-forge
argon2-cffi               20.1.0           py39hbd71b63_2    conda-forge
async_generator           1.10                       py_0    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
attrs                     19.3.0                     py_0    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
bleach                    3.1.5              pyh9f0ad1d_0    conda-forge
blinker                   1.4                        py_1    conda-forge
boost-cpp                 1.74.0               hc6e9bd1_3    conda-forge
brotlipy                  0.7.0           py39h3811e60_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h7f98852_1    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
certifi                   2021.5.30        py39hf3d152e_0    conda-forge
certipy                   0.1.3                      py_0    conda-forge
cffi                      1.14.5           py39he32792d_0    conda-forge
cfitsio                   3.470                hb418390_7    conda-forge
cftime                    1.5.0            py39hce5d2b2_0    conda-forge
chardet                   4.0.0            py39hf3d152e_1    conda-forge
chrpath                   0.16              h7f98852_1002    conda-forge
cryptography              3.4.7            py39hbca0aa6_0    conda-forge
curl                      7.77.0               hea6ffbf_0    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
dcw-gmt                   1.1.4                      1001    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3             py39hde42818_1002    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
ffmpeg                    4.3.1                hca11adc_2    conda-forge
fftw                      3.3.9           nompi_hcdd671c_101    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                  2.10.4               h0708190_1    conda-forge
freexl                    1.0.6                h7f98852_0    conda-forge
fribidi                   1.0.10               h516909a_0    conda-forge
gdal                      3.3.0            py39h409cc32_1    conda-forge
gdk-pixbuf                2.42.6               h04a7f16_0    conda-forge
geos                      3.9.1                h9c3ff4c_2    conda-forge
geotiff                   1.6.0                hcf90da6_5    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
ghostscript               9.54.0               h9c3ff4c_1    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
glib                      2.68.2               h9c3ff4c_2    conda-forge
glib-tools                2.68.2               h9c3ff4c_2    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmt                       6.2.0                h88440e8_0    conda-forge
gnuplot                   5.4.1                hec6539f_2    conda-forge
gnutls                    3.6.13               h85f3911_1    conda-forge
graphicsmagick            1.3.35               h2852e03_2    conda-forge
graphite2                 1.3.13            he1b5a44_1001    conda-forge
greenlet                  1.1.0            py39he80948d_0    conda-forge
gshhg-gmt                 2.3.7             ha770c72_1003    conda-forge
gst-plugins-base          1.18.4               hf529b03_2    conda-forge
gstreamer                 1.18.4               h76c114f_2    conda-forge
gtk2                      2.24.33              h539f30e_1    conda-forge
harfbuzz                  2.8.1                h83ec7ef_0    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
importlib-metadata        4.5.0            py39hf3d152e_0    conda-forge
importlib_metadata        4.5.0                hd8ed1ab_0    conda-forge
ipykernel                 5.5.5            py39hef51801_0    conda-forge
ipython                   7.24.1           py39hef51801_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.3              pyhd3deb0d_0    conda-forge
jedi                      0.18.0           py39hf3d152e_2    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
json-c                    0.15                 h98cffda_0    conda-forge
json5                     0.9.4              pyh9f0ad1d_0    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
jupyter-offlinenotebook   0.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            6.1.6                      py_0    conda-forge
jupyter_core              4.7.1            py39hf3d152e_0    conda-forge
jupyter_server            1.8.0              pyhd8ed1ab_0    conda-forge
jupyter_telemetry         0.0.5                      py_0    conda-forge
jupyterhub-base           1.2.1            py39hf3d152e_0    conda-forge
jupyterhub-singleuser     1.2.1            py39hf3d152e_0    conda-forge
jupyterlab                3.0.7              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.6.0              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.0.0              pyhd8ed1ab_1    conda-forge
kealib                    1.4.14               hcc255d8_2    conda-forge
krb5                      1.19.1               hcc1bbae_0    conda-forge
lame                      3.100             h14c3975_1001    conda-forge
ld_impl_linux-64          2.34                 h53a641e_7    conda-forge
libblas                   3.9.0                9_openblas    conda-forge
libcblas                  3.9.0                9_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcurl                   7.77.0               h2574ce0_0    conda-forge
libdap4                   3.20.6               hd7c4107_2    conda-forge
libedit                   3.1.20191231         h46ee950_1    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-ng                 9.3.0               h2828fa1_19    conda-forge
libgd                     2.3.2                h78a0170_0    conda-forge
libgdal                   3.3.0                h679344c_1    conda-forge
libgfortran-ng            9.3.0               hff62375_19    conda-forge
libgfortran5              9.3.0               hff62375_19    conda-forge
libglib                   2.68.2               h3e27bee_2    conda-forge
libgomp                   9.3.0               h2828fa1_19    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libkml                    1.3.0             h238a007_1013    conda-forge
liblapack                 3.9.0                9_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnetcdf                 4.8.0           nompi_hcd642e3_103    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.15          pthreads_h8fe5266_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libpq                     13.3                 hd57d9b9_0    conda-forge
librttopo                 1.1.0                h1185371_6    conda-forge
libsodium                 1.0.18               h516909a_1    conda-forge
libspatialite             5.0.1                h20cb978_4    conda-forge
libssh2                   1.9.0                hab1572f_4    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
libtiff                   4.2.0                hbd63e13_2    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libvorbis                 1.3.7                he1b5a44_0    conda-forge
libwebp                   1.2.0                h3452ae3_0    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libzip                    1.7.3                he9f05b3_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
mako                      1.1.0                      py_0    conda-forge
markupsafe                2.0.1            py39h3811e60_0    conda-forge
matplotlib-inline         0.1.2              pyhd8ed1ab_2    conda-forge
mistune                   0.8.4           py39h3811e60_1003    conda-forge
mysql-common              8.0.23               ha770c72_2    conda-forge
mysql-libs                8.0.23               h935591d_2    conda-forge
nbclassic                 0.2.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.3              pyhd8ed1ab_0    conda-forge
nbconvert                 6.0.7            py39hf3d152e_3    conda-forge
nbformat                  5.0.7                      py_0    conda-forge
nbresuse                  0.3.3                      py_0    conda-forge
ncurses                   6.2                  he1b5a44_1    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
netcdf4                   1.5.6           nompi_py39hc6dca20_103    conda-forge
nettle                    3.6                  he412f7d_0    conda-forge
notebook                  6.4.0              pyha770c72_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.66                 hb5efdd6_0    conda-forge
nteract_on_jupyter        2.1.3                      py_0    conda-forge
numpy                     1.20.3           py39hdbf815f_1    conda-forge
oauthlib                  3.0.1                      py_0    conda-forge
openh264                  2.1.1                h780b84a_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
packaging                 20.4               pyh9f0ad1d_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandas                    1.2.4            py39hde0f152_0    conda-forge
pandoc                    2.10.1               h516909a_0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.48.5               hb8ff022_0    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pip                       20.1.1                     py_1    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
poppler                   21.03.0              h93df280_0    conda-forge
poppler-data              0.4.10                        0    conda-forge
postgresql                13.3                 h2510834_0    conda-forge
proj                      8.0.0                h277dcde_0    conda-forge
prometheus_client         0.8.0              pyh9f0ad1d_0    conda-forge
prompt-toolkit            3.0.5                      py_1    conda-forge
psutil                    5.8.0            py39h3811e60_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pycurl                    7.43.0.6         py39h72e3413_1    conda-forge
pygments                  2.6.1                      py_0    conda-forge
pygmt                     0.3.1              pyhd8ed1ab_0    conda-forge
pyjwt                     1.7.1                      py_0    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyrsistent                0.17.3           py39h3811e60_2    conda-forge
pysocks                   1.7.1            py39hf3d152e_3    conda-forge
python                    3.9.4           hffdb5ce_0_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-editor             1.0.4                      py_0    conda-forge
python-json-logger        0.1.11                     py_0    conda-forge
python_abi                3.9                      1_cp39    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyzmq                     22.1.0           py39h37b5a0c_0    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
ruamel.yaml               0.17.7           py39h3811e60_0    conda-forge
ruamel.yaml.clib          0.2.2            py39h3811e60_2    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                49.6.0           py39hf3d152e_3    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sniffio                   1.2.0            py39hf3d152e_1    conda-forge
sqlalchemy                1.4.17           py39h3811e60_0    conda-forge
sqlite                    3.35.5               h74cdb3f_0    conda-forge
terminado                 0.10.0           py39hf3d152e_0    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tiledb                    2.2.9                h91fcb0e_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
traitlets                 5.0.5                      py_0    conda-forge
tzcode                    2021a                h7f98852_1    conda-forge
tzdata                    2021a                he74cb21_0    conda-forge
urllib3                   1.25.10                    py_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          0.57.0           py39hf3d152e_4    conda-forge
wheel                     0.34.2                     py_1    conda-forge
widgetsnbextension        3.5.1            py39hf3d152e_4    conda-forge
x264                      1!161.3030           h7f98852_0    conda-forge
xarray                    0.18.2             pyhd8ed1ab_0    conda-forge
xerces-c                  3.2.3                h9d8b166_2    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.1                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_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            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zeromq                    4.3.4                h9c3ff4c_0    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.9                ha95c52a_0    conda-forge

[joa-quim]

Bumping to Julia 1.6 (even 1.5) should have fixed this. It did fix in the CI machine when I updated it to Ubuntu 2020

[seisman]

GMT.jl now works well on Binder. Closing.