Comments (6)
seisman
commented on May 27, 2024
But we can't control the Ubuntu version we're using on Binder...
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joa-quim
commented on May 27, 2024
There is nothing Julia specific in this error. It should be a problem for PyGMT and GMT Binder sets. Don't you see it?
from try-gmt.
seisman
commented on May 27, 2024
Yes, the same problem. Something wrong with conda-forge's packages.
from try-gmt.
weiji14
commented on May 27, 2024
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
from try-gmt.
joa-quim
commented on May 27, 2024
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
from try-gmt.
seisman
commented on May 27, 2024
GMT.jl now works well on Binder. Closing.
from try-gmt.
Related Issues (12)
- Need feedbacks on the Jupyter lab for trying GMT and its wrappers online HOT 11
- Julia version is still 1.3.1
- pygmt import error on google colaboratory HOT 7
- Binder repository for interactive GMT tutorials HOT 4
- Install optional geopandas dependency on try-gmt?
- Don't change links that the user is about to click HOT 2
- Add run GMT in bash instructions HOT 4
- Google Colab Implementation HOT 5
- New example to try pygmt on google colab. HOT 3
- The Julia example doesn't work HOT 2
- Improve the speed for loading the GMT.jl package HOT 3
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