import error with freshly created vcs/cdms2

doutriaux1 commented 5 years ago

ImportError: dlopen(/Users/doutriaux1/miniconda3/envs/vcdt/lib/python3.6/site-packages/cdtime/_cdtime.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libc++.1.dylib
  Referenced from: /Users/doutriaux1/miniconda3/envs/vcdt/lib/python3.6/site-packages/cdtime/_cdtime.cpython-36m-darwin.so
  Reason: image not found

conda list:

# packages in environment at /Users/doutriaux1/miniconda3/envs/vcdt:
#
# Name                    Version                   Build  Channel
alembic                   0.9.9                      py_0    conda-forge
appnope                   0.1.0                 py36_1000    conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     18.2.0                     py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
blas                      1.0                         mkl    defaults
bleach                    3.0.2                      py_1    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cdat_info                 8.0.2018.11.28.19.22.gb6530fa            py_0    cdat/label/nightly
cdms2                     3.1.0.2018.11.29.11.23.g5a83dd4  py36hdde6e19_0    cdat/label/nightly
cdtime                    3.1.0.2018.11.01.10.48.gb8c370e  py36hdc02c5d_0    cdat/label/nightly
cdutil                    8.0.2018.11.12.19.20.g3bd6383            py_0    cdat/label/nightly
certifi                   2018.11.29            py36_1000    conda-forge
cffi                      1.11.5           py36h5e8e0c9_1    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
clapack                   3.2.1                h470a237_1    conda-forge
configurable-http-proxy   3.1.0                   node8_1    conda-forge
cryptography              2.3.1            py36hdffb7b8_0    conda-forge
cryptography-vectors      2.3.1                 py36_1000    conda-forge
curl                      7.63.0               h74213dd_0    conda-forge
decorator                 4.3.0                      py_0    conda-forge
distarray                 2.12.2                     py_1    conda-forge
dv3d                      8.0.2018.12.15.10.52.g215c720            py_0    cdat/label/nightly
entrypoints               0.2.3                 py36_1002    conda-forge
esmf                      7.1.0r               h35eb876_3    conda-forge
esmpy                     7.1.0r                   py36_1    conda-forge
expat                     2.2.5                hfc679d8_2    conda-forge
ffmpeg                    4.0.2                ha0c5888_2    conda-forge
freetype                  2.9.1                h6debe1e_4    conda-forge
future                    0.17.0                py36_1000    conda-forge
g2clib                    1.6.0                         3    conda-forge
genutil                   8.1.2018.10.17.14.26.ga5756e2.npy1.14  py36h776bbcc_0    cdat/label/nightly
gettext                   0.19.8.1             h1f1d5ed_1    conda-forge
ghostscript               9.22                 hfc679d8_1    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
gnutls                    3.5.19               h2a4e5f8_1    conda-forge
hdf4                      4.2.13               h951d187_2    conda-forge
hdf5                      1.10.3               hc401514_2    conda-forge
idna                      2.8                   py36_1000    conda-forge
intel-openmp              2019.1                      144    defaults
ipykernel                 5.1.0           py36h24bf2e0_1001    conda-forge
ipython                   7.2.0           py36h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jasper                    1.900.1              hff1ad4c_5    conda-forge
jedi                      0.13.2                py36_1000    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
jsonschema                3.0.0a3               py36_1000    conda-forge
jupyter-vcdat             2.0.0.2018.12.17.23.37.g0e0419d            py_0    cdat/label/nightly
jupyter_client            5.2.4                      py_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyterhub                0.9.4                 py36_1000    conda-forge
jupyterlab                0.35.4                   py36_0    conda-forge
jupyterlab_server         0.2.0                      py_0    conda-forge
krb5                      1.16.2               hbb41f41_0    conda-forge
lapack                    3.6.1                         1    conda-forge
libcdms                   3.0.2018.10.17.14.17.g4f79235      hdc02c5d_0    cdat/label/nightly
libcf                     3.0.2018.06.27.19.10.g994aa30  py36h1de35cc_0    cdat/label/nightly
libcurl                   7.63.0               hbdb9355_0    conda-forge
libdrs                    3.0.2018.10.18.14.41.g36264ac      hdc02c5d_0    cdat/label/nightly
libdrs_f                  3.0.2018.10.18.14.41.g36264ac      hdc02c5d_0    cdat/label/nightly
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgfortran               3.0.1                h93005f0_2    defaults
libiconv                  1.15                 h470a237_3    conda-forge
libnetcdf                 4.6.1               h350cafa_11    conda-forge
libpng                    1.6.36               ha92aebf_0    conda-forge
libsodium                 1.0.16               h470a237_1    conda-forge
libssh2                   1.8.0                h5b517e9_3    conda-forge
libtiff                   4.0.10               he6b73bb_1    conda-forge
mako                      1.0.7                      py_1    conda-forge
markupsafe                1.1.0            py36h470a237_0    conda-forge
mistune                   0.8.4            py36h470a237_0    conda-forge
mkl                       2019.1                      144    defaults
mkl_fft                   1.0.10                   py36_0    conda-forge
mkl_random                1.0.2                    py36_0    conda-forge
mpi                       1.0                       mpich    conda-forge
mpich                     3.2.1                h26a2512_7    conda-forge
nb_conda                  2.2.1                    py36_0    conda-forge
nb_conda_kernels          2.2.0                 py36_1000    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1                  hfc679d8_2    conda-forge
netcdf-fortran            4.4.4               h71ea97b_10    conda-forge
nettle                    3.3                           0    conda-forge
nodejs                    8.10.0                        0    conda-forge
notebook                  5.7.4                 py36_1000    conda-forge
numpy                     1.15.4           py36hacdab7b_0    defaults
numpy-base                1.15.4           py36h6575580_0    defaults
openh264                  1.8.0                hd28b015_0    conda-forge
openssl                   1.0.2p               h470a237_1    conda-forge
ossuuid                   1.6.2                hfc679d8_0    conda-forge
pamela                    0.3.0                   py_1001    conda-forge
pandoc                    2.5                           0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.3.1                      py_0    conda-forge
pexpect                   4.6.0                 py36_1000    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
prometheus_client         0.5.0                      py_0    conda-forge
prompt_toolkit            2.0.7                      py_0    conda-forge
ptyprocess                0.6.0                 py36_1000    conda-forge
pycparser                 2.19                       py_0    conda-forge
pycurl                    7.43.0.2         py36hdbc3d79_0    defaults
pygments                  2.3.1                      py_0    conda-forge
pyopenssl                 18.0.0                py36_1000    conda-forge
pyrsistent                0.14.7           py36h470a237_0    conda-forge
pysocks                   1.6.8                 py36_1002    conda-forge
python                    3.6.7                h5001a0f_1    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
python-editor             1.0.3                      py_0    conda-forge
python-oauth2             1.1.0                    py36_0    conda-forge
pyzmq                     17.1.2           py36hae99301_1    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
requests                  2.21.0                py36_1000    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                40.6.3                   py36_0    conda-forge
six                       1.12.0                py36_1000    conda-forge
sqlalchemy                1.2.15           py36h470a237_0    conda-forge
sqlite                    3.26.0               hb1c47c0_0    conda-forge
terminado                 0.8.1                 py36_1001    conda-forge
testpath                  0.4.2                 py36_1000    conda-forge
tk                        8.6.9                ha92aebf_0    conda-forge
toolchain                 2.3.0                         0    conda-forge
tornado                   5.1.1            py36h470a237_0    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
udunits2                  2.2.27.6             h3a4f0e9_1    conda-forge
urllib3                   1.24.1                py36_1000    conda-forge
vcs                       8.0.2018.12.18.00.02.gc7a97688            py_0    cdat/label/nightly
vtk-cdat                  8.2.0.rc2.289.8.0.2018.12.12.20.03.g14c0bb696d  py36h413fb2d_0    cdat/label/nightly
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
x264                      1!152.20180717       h470a237_1    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
zeromq                    4.2.5                hfc679d8_6    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

doutriaux1 commented 5 years ago

rebuilding cdtime from source locally fixes the issue.

dnadeau4 commented 5 years ago

@doutriaux1 you don't have "clang" or "gcc" in your environment. Could that be the reason for Library not loaded: @rpath/libc++.1.dylib

doutriaux1 commented 5 years ago

@dnadeau4 rebuilding master broke linux... I removed the nighlty for linux. It does looks like it fixed mac though.

dnadeau4 commented 5 years ago

It has something to do with using fortran code no compiled with gcc7 (version 7). I saw this before, it is fixed in conda-forge, but I need to revise all the circleci for each fortran code. (cdms look fine, might be libdrs)

doutriaux1 commented 5 years ago

possibly, libdrs_f is the one that uses fortran, then it probably propagates to libcdms

github-actions[bot] commented 4 years ago

Marking issue as stale, since there has been no activity in 30 days.

Unless the issue is updated or the 'stale' tag is removed, this issue will be closed in 7 days.

CDAT / cdtime

import error with freshly created vcs/cdms2 #33