Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

GMT.jl is broken on Binder #15

Closed
joa-quim opened this issue Feb 9, 2021 · 6 comments
Closed

GMT.jl is broken on Binder #15

joa-quim opened this issue Feb 9, 2021 · 6 comments
Labels
bug Something isn't working

Comments

@joa-quim
Copy link
Member

joa-quim commented Feb 9, 2021

image

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
Copy link
Member

seisman commented Feb 9, 2021

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

@joa-quim
Copy link
Member Author

joa-quim commented Feb 9, 2021

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
Copy link
Member

seisman commented Feb 9, 2021

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

@weiji14
Copy link
Member

weiji14 commented Jun 6, 2021 •
edited
Loading

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

@weiji14 weiji14 mentioned this issue Jun 6, 2021
Merged
@weiji14 weiji14 added the bug Something isn't working label Jun 6, 2021
@joa-quim
Copy link
Member Author

joa-quim commented Jun 6, 2021

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
Copy link
Member

seisman commented May 12, 2022

GMT.jl now works well on Binder. Closing.

@seisman seisman closed this as completed May 12, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@joa-quim @seisman @weiji14