import error with freshly created vcs/cdms2
Closed this issue · 6 comments
doutriaux1 commented
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
rebuilding cdtime from source locally fixes the issue.
dnadeau4 commented
@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
@dnadeau4 rebuilding master broke linux... I removed the nighlty for linux. It does looks like it fixed mac though.
dnadeau4 commented
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
possibly, libdrs_f is the one that uses fortran, then it probably propagates to libcdms
github-actions commented
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.