Closed keflavich closed 7 years ago
Unfortunately this error is something that happens generically when the binary modules aren't working right. Can you tell me your operating system version and the output of conda info
and conda list
when you're set up for the environment that has casa-python
installed?
conda list
:
# packages in environment at /Users/adam/anaconda/envs/astropy27:
#
alabaster 0.7.6 py27_0
antfs-cli 0.2 <pip>
apipkg 1.4 <pip>
appdirs 1.4.3 <pip>
appnope 0.1.0 py27_0
appnope-0.0.7 dev <pip>
asciitable 0.8.0 <pip>
astroid 1.3.8 <pip>
astroML-0.3 git <pip>
astropy 1.0.4 np19py27_0
astroquery 0.3.dev2795 <pip>
astroquery 0.2.dev1311 <pip>
astroquery 0.3.dev2792 <pip>
astroquery 0.3.dev <pip>
AtomPy 0.5.1.1 <pip>
ATpy 0.9.6 <pip>
ATpy 0.9.7 <pip>
babel 2.1.1 py27_0
backports 1.0 py27_0
backports_abc 0.4 py27_0
beautiful-soup 4.3.1 py27_0 <unknown>
BeautifulSoup 3.2.1 <pip>
beautifulsoup4 4.3.2 <pip>
beautifulsoup4 4.6.0 py27_0
bleach 1.4.1 <pip>
bokeh 0.8.2 np19py27_0
boost 1.63.0 np112py27_6 conda-forge
boost-cpp 1.63.0 2 conda-forge
Bottleneck 1.0.0 <pip>
bottleneck 0.8.0 np18py27_0 https://conda.binstar.org/asmeurer
bzip2 1.0.6 1 conda-forge
casa-nrao-casacore 4.6.0 6 pkgw-forge
casa-python 4.7.2 np112py27_3 pkgw-forge
casa-tools 4.7.2 1 pkgw-forge
casacore 2.2.0 0 conda-forge
cfitsio 3.410 2 conda-forge
cloog 0.18.0 0
colorama 0.3.3 py27_0
colorspacious 0.1.0 <pip>
coords 0.37 <pip>
coverage 3.7.1 py27_0
coveralls 0.4.2 <pip>
cycler 0.10.0 py27_0
cython 0.25.2 py27_0
d2to1 0.2.7 <pip>
dask 0.7.0 <pip>
dateutil 2.1 py27_2 <unknown>
dbus 1.10.10 3 conda-forge
dbus-client 1.10.6 1 pkgw
dbus-cxx 0.9.1 0 pkgw
decorator 4.0.4 py27_0
DESPOTIC 2.0 <pip>
DESPOTIC 2.1 <pip>
distribute 0.6.45 py27_1
docopt 0.6.2 <pip>
docutils 0.11 <pip>
docutils 0.12 py27_0
doge 3.5.0 <pip>
emcee 2.1.0 <pip>
enum34 1.1.6 py27_0
execnet 1.4.1 <pip>
expat 2.1.0 1 pkgw
eyeD3 0.7.5 <pip>
fastcache 1.0.2 py27_0
feedgenerator 1.7 <pip>
fftw 3.3.4 1 pkgw
FITS-tools 0.0.dev <pip>
flake8 2.4.1 <pip>
Flask 0.10.1 <pip>
flask 0.10.1 py27_1
flickrapi 2.0 <pip>
freetype 2.7 1 conda-forge
funcsigs 0.4 <pip>
functools32 3.2.3.2 py27_0
functools32-3.2.3 1 <pip>
futures 3.0.2 <pip>
gammapy 0.1 <pip>
gausspy 1.0 <pip>
gcc 4.8.5 3
gdata 2.0.18 <pip>
get_terminal_size 1.0.0 py27_0
gettext 0.19.6 0 pkgw
gevent 1.0.1 py27_0
gevent-websocket 0.9.3 py27_0
ginga 2.3.20150415221522 <pip>
glib 2.46.2 2 pkgw
glueviz 0.5.3 np19py27_1
gmp 5.1.2 6
google-api-python-client 1.2 <pip>
grasp 0.3.2 <pip>
greenlet 0.4.6 py27_0
gsl 2.2.1 1 conda-forge
gunicorn 19.3.0 <pip>
h2co_modeling 0.1 <pip>
h5py 2.7.0 np112py27_0 conda-forge
hdf5 1.8.17 9 conda-forge
healpy 1.8.5 <pip>
higal-sedfitter 0.0.dev <pip>
higal-sedfitter 0.0.dev59 <pip>
higal-sedfitter 0.0.dev50 <pip>
higal-sedfitter 0.0.dev36 <pip>
html5lib 0.999 py27_0
html5lib 1.0b3 <pip>
httplib2 0.9 <pip>
icu 58.1 1 conda-forge
image-registration 0.2.1 <pip>
imexam 0.3.dev <pip>
inflect 0.2.5 <pip>
iotop 0.6 <pip>
ipdb 0.8 <pip>
ipykernel 4.1.1 py27_0
ipython 5.3.0 py27_0
ipython-notebook 4.0.4 py27_0
ipython-qtconsole 4.0.1 py27_0
ipython_genutils 0.1.0 py27_0
ipywidgets 4.1.0 py27_0
isl 0.12.2 1
itsdangerous 0.24 py27_0
itsdangerous 0.24 <pip>
jbig 2.1 0
jedi 0.9.0 <pip>
Jinja2 2.7.3 <pip>
jinja2 2.9.6 py27_0
jpeg 9b 0
jsonschema 2.4.0 py27_0
jupyter 1.0.0 py27_0
jupyter_client 4.1.1 py27_0
jupyter_console 4.0.3 py27_0
jupyter_core 4.0.6 py27_0
kdist 0.1 <pip>
keyring 3.7 py27_0
keyring 3.8 <pip>
keyring 5.0 <pip>
lcms 1.19 0
libffi32 3.2.1 0 pkgw
libgfortran 3.0.0 0 conda-forge
libkd 1.0 <pip>
libpng 1.6.28 0 conda-forge
libsakura 3.0.0 0 conda-forge
libsodium 0.4.5 0
libtiff 4.0.6 3
libxcb 1.12 1 conda-forge
libxml2 2.9.0 1
libxslt 1.1.28 2 <unknown>
line_profiler 1.0b3 <pip>
lineid_plot 0.2 <pip>
lmfit 0.8.3 <pip>
logilab-common 1.0.2 <pip>
lolcat 0.42.42 <pip>
lxml 3.3.5 py27_0
MarkupSafe 0.23 <pip>
markupsafe 0.23 py27_0
matplotlib 2.0.2 np112py27_0 conda-forge
mccabe 0.3.1 <pip>
memory-profiler 0.39 <pip>
mercurial 3.0 py27_0
mistune 0.7.1 py27_0
mkl 2017.0.1 0
mock 1.3.0 <pip>
modern-xorg-stack 2015.12 2 pkgw
montage-wrapper 0.9.8.dev197 <pip>
montage-wrapper 0.9.9.dev237 <pip>
montage-wrapper 0.9.9.dev233 <pip>
mpc 1.0.1 0
mpfr 3.1.2 0
mpld3 0.2 <pip>
mpmath 0.19 py27_1
multiplot 1.0 <pip>
musepy 0.0.dev0 <pip>
natsort 4.0.3 py27_0
natsort 4.0.0 <pip>
nbconvert 4.0.0 py27_0
nbformat 4.0.1 py27_0
ncurses 5.9 10
networkx 1.10 py27_0
nose 1.3.3 py27_0
notebook 4.0.6 py27_0
ntplib 0.3.2 <pip>
numpy 1.7.1 <pip>
numpy 1.12.0 py27_0
numpy 1.9.1 <pip>
numpy 1.10.1 <pip>
oauth2 1.5.211 <pip>
oauthlib 0.7.2 <pip>
olefile 0.44 py27_0
openant 0.3 <pip>
openblas 0.2.19 2 conda-forge
opencv 2.4.8 np17py27_2
openmpi 1.6.3 0
openssl 1.0.2d 0
packaging 16.8 <pip>
palettable 2.1.1 <pip>
pandas 0.20.1 np112py27_0
pandas 0.14.1 <pip>
path.py 8.1.2 py27_1
pathlib 1.0.1 py27_0 conda-forge
pathlib2 2.2.1 py27_0
patsy 0.3.0 <pip>
pbr 1.4.0 <pip>
pdfnup 0.4.1 <pip>
pep8 1.5.7 <pip>
pexpect 3.3 py27_0
pgplot 5.2.2 5 pkgw
photutils 0.0.dev209 <pip>
pickleshare 0.5 py27_0
pil 1.1.7 py27_1
pillow 4.1.1 py27_0 conda-forge
pip 1.0.2 <pip>
pip 7.1.2 py27_0
plasTeX 1.0 <pip>
plfit 1.0.2 <pip>
plotly 1.0.30 <pip>
powerlaw 1.3.2 <pip>
progressbar 2.3 <pip>
prompt_toolkit 1.0.14 py27_0
psrecord 0.1.0 <pip>
psutil 2.1.1 <pip>
psycopg2 2.6 py27_1
ptyprocess 0.5 py27_0
pvextractor 0.0.dev256 <pip>
pvextractor 0.0.dev233 <pip>
pvextractor 0.0.dev241 <pip>
pvextractor 0.0.dev255 <pip>
pwkit 0.8.4 py27_1 pkgw-forge
py 1.4.33 <pip>
py 1.4.20 py27_0 <unknown>
PyAVM 0.9.3.dev <pip>
PyAVM 0.9.1 <pip>
pyCloudy 0.8.50 <pip>
pyds9 1.7 <pip>
PyFFTW3 0.2.1 <pip>
pyfits 3.2.4 <pip>
pyflakes 0.8.1 <pip>
PyGithub 1.25.2 <pip>
pyglut 1.0.0 <pip>
pygments 2.0.2 py27_0
Pygments 1.6 <pip>
pyjs9 1.0 <pip>
pylint 1.4.4 <pip>
pymc 2.2 <pip>
PyNeb 1.0.2 <pip>
pyparsing 1.5.7 <pip>
pyparsing 2.0.3 py27_0
pyparsing 2.2.0 <pip>
pyPdf 1.13 <pip>
pyqt 5.6.0 py27_2
pyradex 0.4.1dev <pip>
pyregion 1.1.2 <pip>
pyregion 2.0.dev0 <pip>
pyside 1.1.2 py27_1 <unknown>
pytest 2.5.2 py27_0 <unknown>
pytest 3.0.7 <pip>
pytest-arraydiff 0.1 <pip>
pytest-cache 1.0 <pip>
pytest-mpl 0.7 py27_0 astropy
pytest-pep8 1.0.6 <pip>
pytest-runner 2.11.1 <pip>
python 2.7.11 0
python-dateutil 2.2 <pip>
python-dateutil 2.4.2 py27_0
python-flickr 0.3.2 <pip>
python-magic 0.4.6 <pip>
python.app 1.2 py27_4
pytz 2017.2 py27_0
pytz 2014.7 <pip>
pyusb 1.0.0b2 <pip>
pywavelets 0.5.2 np112py27_0
pyyaml 3.12 py27_0
pyzmq 14.7.0 py27_1
qt 5.6.2 1 conda-forge
qt-dbus-component 4.8.7 1 pkgw
qt4 4.8.7 2 pkgw-forge
qtconsole 4.1.0 py27_0
qwt5 5.2.3 1 pkgw
radio_beam 0.0 <pip>
radmc3dPy 0.25 <pip>
radmc3dPy 0.28.2 <pip>
rauth 0.7.1 <pip>
readline 6.2 2 <unknown>
regex 2015.05.28 <pip>
requests 2.5.1 <pip>
requests 2.7.0 py27_0
requests 2.7.0 <pip>
requests-futures 0.9.5 <pip>
requests-oauthlib 0.5.0 <pip>
requests-toolbelt 0.4.0 <pip>
rpfits 2.23 6 pkgw
scandir 1.5 py27_0
scikit-image 0.13.0 np112py27_0
scikit-learn 0.18.1 np112py27_1
scikit-learn 0.15.2 <pip>
scimes 0.1.1 <pip>
scipy 0.19.0 np112py27_0
sep 0.3.0 <pip>
sep 0.2.0 <pip>
setuptools 27.2.0 py27_0
setuptools 35.0.2 <pip>
Shapely 1.5.2 <pip>
shiboken 1.1.2 py27_0 <unknown>
simplegeneric 0.8.1 py27_0
simplejson 3.7.3 <pip>
singledispatch 3.4.0.3 py27_0
sip 4.18 py27_0
six 1.9.0 <pip>
six 1.10.0 <pip>
six 1.10.0 py27_0
sklearn 0.0 <pip>
SLUGPY 2.1 <pip>
snakeviz 0.4.0 <pip>
snowballstemmer 1.2.0 py27_0
specreduce 0.0.dev <pip>
spectral-cube 0.3.1.dev938 <pip>
spectral-cube 0.3.1.dev922 <pip>
spectral_cube 0.1.dev <pip>
Sphinx 1.2.2 <pip>
sphinx 1.3.1 py27_0
sphinx_rtd_theme 0.1.7 py27_0
sqlalchemy 1.0.5 py27_0
sqlite 3.8.4.1 1
ssl_match_hostname 3.4.0.2 py27_0 <unknown>
starlink-pyast 2.6 <pip>
statsmodels 0.5.0 <pip>
stsci.distutils 0.3.2 <pip>
stsci.tools 3.2.2 <pip>
subprocess32 3.2.7 py27_0
sympy 0.7.6.1 py27_0
terminado 0.5 py27_1
thingking 1.0.2 <pip>
tk 8.5.18 0
toolz 0.7.4 <pip>
tornado 4.3 py27_0
traitlets 4.3.2 py27_0
triangle-plot 0.0.6 <pip>
tzlocal 1.2 <pip>
ujson 1.33 py27_0
Unidecode 0.04.16 <pip>
vamdclib 0.1 <pip>
viscm 0.3 <pip>
vtk 5.10.1 py27_0
Wand 0.3.8 <pip>
wcslib 5.16 1 conda-forge
wcwidth 0.1.7 py27_0
werkzeug 0.10.4 py27_0
Werkzeug 0.10.4 <pip>
wheel 0.26.0 py27_1
WTForm 1.0 <pip>
WTForms 2.0.2 <pip>
wxpython 3.0 py27_0
xerces-c28 2.8.0 1 pkgw
xlrd 0.9.3 <pip>
xlwt 0.7.5 <pip>
xmltodict 0.9.2 <pip>
xorg-kbproto 1.0.7 1 conda-forge
xorg-libx11 1.6.4 6 conda-forge
xorg-libxau 1.0.8 3 conda-forge
xorg-libxdmcp 1.1.2 3 conda-forge
xorg-libxext 1.3.3 2 conda-forge
xorg-xextproto 7.3.0 1 conda-forge
xorg-xproto 7.0.31 6 conda-forge
xz 5.2.2 1
yaml 0.1.6 0
yt 3.2.2 <pip>
yt 3.2.2 py27_0
yt 3.3.dev0 <pip>
yt 3.0 <pip>
zeromq 4.1.3 0
zlib 1.2.8 0
Hoo boy, OK. The environment that you used for the conda list
has a lot of older versions of packages that might be causing problems. Unfortunately conda
doesn't support package conflicts so we don't really have a mechanism for automatically preventing multiple installations of such things.
It is possible to work through these by uninstalling the old packages and then reinstalling the newer versions with the -f
option to make sure that the files get recreated, but that's a bit of a risky operation. I think it would be safer to create a new environment that's populated afresh.
Can you try creating a new environment with a minimal installation, then installing casa-python
in that one? If that works, I think the older packages are the problem. The ones that come from the pkgw
channel, rather than the pkgw-forge
channel, are probably the main culprits.
tried it, no dice:
cyg ~$ conda create -n casa matplotlib=1.5 astropy numpy scipy python=2.7
Fetching package metadata .................
Solving package specifications: .
Package plan for installation in environment /Users/adam/anaconda/envs/casa:
The following NEW packages will be INSTALLED:
astropy: 1.3.2-np111py27_0
cycler: 0.10.0-py27_0
freetype: 2.5.5-2
icu: 54.1-0
libpng: 1.6.27-0
matplotlib: 1.5.3-np111py27_1
mkl: 2017.0.1-0
numpy: 1.11.3-py27_0
openssl: 1.0.2k-2
pip: 9.0.1-py27_1
pyparsing: 2.1.4-py27_0
pyqt: 5.6.0-py27_2
python: 2.7.13-0
python-dateutil: 2.6.0-py27_0
pytz: 2017.2-py27_0
qt: 5.6.2-1
readline: 6.2-2
scipy: 0.19.0-np111py27_0
setuptools: 27.2.0-py27_0
sip: 4.18-py27_0
six: 1.10.0-py27_0
sqlite: 3.13.0-0
tk: 8.5.18-0
wheel: 0.29.0-py27_0
zlib: 1.2.8-3
openssl-1.0.2k 100% |#########################################################################################################################| Time: 0:00:00 3.83 MB/s
qt-5.6.2-1.tar 100% |#########################################################################################################################| Time: 0:00:07 9.62 MB/s
#
# To activate this environment, use:
# > source activate casa
#
# To deactivate this environment, use:
# > source deactivate casa
#
cyg ~$ conda install -n casa -c conda-forge -c pkgw-forge casa-python=4.7.2
Fetching package metadata .....................
Solving package specifications: .
Package plan for installation in environment /Users/adam/anaconda/envs/casa:
The following NEW packages will be INSTALLED:
backports_abc: 0.5-py27_0 conda-forge
boost: 1.63.0-np112py27_6 conda-forge
boost-cpp: 1.63.0-2 conda-forge
bzip2: 1.0.6-1 conda-forge
casa-python: 4.7.2-np112py27_4 pkgw-forge
casa-tools: 4.7.2-1 pkgw-forge
casacore: 2.2.0-0 conda-forge
certifi: 2017.4.17-py27_0 conda-forge
cfitsio: 3.410-2 conda-forge
dbus: 1.10.10-3 conda-forge
dbus-cxx: 0.9.1-1 conda-forge
expat: 2.1.0-2 conda-forge
fftw: 3.3.6-0 conda-forge
functools32: 3.2.3.2-py27_1 conda-forge
gettext: 0.19.7-1 conda-forge
glib: 2.51.4-0 conda-forge
gsl: 2.2.1-1 conda-forge
hdf5: 1.8.17-9 conda-forge
jpeg: 9b-0 conda-forge
libffi: 3.2.1-3 conda-forge
libgfortran: 3.0.0-0 conda-forge
libiconv: 1.14-4 conda-forge
libsakura: 3.0.0-0 conda-forge
libtiff: 4.0.6-7 conda-forge
libxcb: 1.12-1 conda-forge
libxml2: 2.9.4-4 conda-forge
libxslt: 1.1.29-3 conda-forge
ncurses: 5.9-10 conda-forge
openblas: 0.2.19-2 conda-forge
pcre: 8.39-0 conda-forge
pgplot: 5.2.2-2 conda-forge
qt4: 4.8.7-2 pkgw-forge
qwt5: 5.2.3-4 pkgw-forge
rpfits: 2.24-1 conda-forge
singledispatch: 3.4.0.3-py27_0 conda-forge
ssl_match_hostname: 3.5.0.1-py27_1 conda-forge
subprocess32: 3.2.7-py27_0 conda-forge
tornado: 4.5.1-py27_0 conda-forge
wcslib: 5.16-1 conda-forge
xerces-c28: 2.8.0-0 conda-forge
xorg-kbproto: 1.0.7-1 conda-forge
xorg-libx11: 1.6.4-6 conda-forge
xorg-libxau: 1.0.8-3 conda-forge
xorg-libxdmcp: 1.1.2-3 conda-forge
xorg-libxext: 1.3.3-2 conda-forge
xorg-xextproto: 7.3.0-1 conda-forge
xorg-xproto: 7.0.31-6 conda-forge
xz: 5.2.2-0 conda-forge
The following packages will be UPDATED:
freetype: 2.5.5-2 --> 2.7-1 conda-forge
icu: 54.1-0 --> 58.1-1 conda-forge
libpng: 1.6.27-0 --> 1.6.28-0 conda-forge
matplotlib: 1.5.3-np111py27_1 --> 2.0.2-np112py27_0 conda-forge
numpy: 1.11.3-py27_0 --> 1.12.1-py27_0
scipy: 0.19.0-np111py27_0 --> 0.19.0-np112py27_0
The following packages will be SUPERSEDED by a higher-priority channel:
astropy: 1.3.2-np111py27_0 --> 1.3.2-np112py27_0 conda-forge
qt: 5.6.2-1 --> 5.6.2-1 conda-forge
expat-2.1.0-2. 100% |#########################################################################################################################| Time: 0:00:00 723.30 kB/s
gettext-0.19.7 100% |#########################################################################################################################| Time: 0:00:00 4.99 MB/s
jpeg-9b-0.tar. 100% |#########################################################################################################################| Time: 0:00:00 51.02 MB/s
libffi-3.2.1-3 100% |#########################################################################################################################| Time: 0:00:00 22.22 MB/s
libiconv-1.14- 100% |#########################################################################################################################| Time: 0:00:01 748.72 kB/s
ncurses-5.9-10 100% |#########################################################################################################################| Time: 0:00:00 2.13 MB/s
pcre-8.39-0.ta 100% |#########################################################################################################################| Time: 0:00:00 1.85 MB/s
xerces-c28-2.8 100% |#########################################################################################################################| Time: 0:00:00 3.47 MB/s
xz-5.2.2-0.tar 100% |#########################################################################################################################| Time: 0:00:00 2.95 MB/s
glib-2.51.4-0. 100% |#########################################################################################################################| Time: 0:00:01 4.65 MB/s
libtiff-4.0.6- 100% |#########################################################################################################################| Time: 0:00:00 5.54 MB/s
libxml2-2.9.4- 100% |#########################################################################################################################| Time: 0:00:00 3.26 MB/s
rpfits-2.24-1. 100% |#########################################################################################################################| Time: 0:00:00 35.75 MB/s
backports_abc- 100% |#########################################################################################################################| Time: 0:00:00 4.10 MB/s
certifi-2017.4 100% |#########################################################################################################################| Time: 0:00:00 560.26 kB/s
dbus-cxx-0.9.1 100% |#########################################################################################################################| Time: 0:00:00 837.27 kB/s
functools32-3. 100% |#########################################################################################################################| Time: 0:00:00 14.78 MB/s
libxslt-1.1.29 100% |#########################################################################################################################| Time: 0:00:00 871.20 kB/s
numpy-1.12.1-p 100% |#########################################################################################################################| Time: 0:00:00 5.68 MB/s
ssl_match_host 100% |#########################################################################################################################| Time: 0:00:00 8.14 MB/s
subprocess32-3 100% |#########################################################################################################################| Time: 0:00:00 376.74 kB/s
astropy-1.3.2- 100% |#########################################################################################################################| Time: 0:00:01 4.14 MB/s
pgplot-5.2.2-2 100% |#########################################################################################################################| Time: 0:00:00 4.89 MB/s
qt-5.6.2-1.tar 100% |#########################################################################################################################| Time: 0:00:07 8.83 MB/s
singledispatch 100% |#########################################################################################################################| Time: 0:00:00 11.70 MB/s
tornado-4.5.1- 100% |#########################################################################################################################| Time: 0:00:00 2.03 MB/s
casa-python-4. 100% |#########################################################################################################################| Time: 0:00:01 6.19 MB/s
If this is your first install of dbus, automatically load on login with:
mkdir -p ~/Library/LaunchAgents
cp /Users/adam/anaconda/envs/casa/org.freedesktop.dbus-session.plist ~/Library/LaunchAgents/
launchctl load -w ~/Library/LaunchAgents/org.freedesktop.dbus-session.plist
If this is an upgrade and you already have the org.freedesktop.dbus-session.plist loaded:
launchctl unload -w ~/Library/LaunchAgents/org.freedesktop.dbus-session.plist
cp /Users/adam/anaconda/envs/casa/org.freedesktop.dbus-session.plist ~/Library/LaunchAgents/
launchctl load -w ~/Library/LaunchAgents/org.freedesktop.dbus-session.plist
cyg ~$ source activate casa
cyg ~$ python -c "import casac"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/adam/anaconda/envs/casa/lib/python2.7/site-packages/casac.py", line 1, in <module>
import __casac__
File "/Users/adam/anaconda/envs/casa/lib/python2.7/site-packages/__casac__/__init__.py", line 51, in <module>
from . import atmosphere
File "/Users/adam/anaconda/envs/casa/lib/python2.7/site-packages/__casac__/atmosphere.py", line 17, in <module>
_atmosphere = swig_import_helper()
File "/Users/adam/anaconda/envs/casa/lib/python2.7/site-packages/__casac__/atmosphere.py", line 16, in swig_import_helper
return importlib.import_module('_atmosphere')
File "/Users/adam/anaconda/envs/casa/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
ImportError: No module named _atmosphere
cyg ~$ which python
/Users/adam/anaconda/envs/casa/bin/python
Ah, bummer. With this new casa
environment activated, can you run:
cd /Users/adam/anaconda/envs/casa/lib/python2.7/site-packages/__casac__
python -c 'import _atmosphere'
And send me the exact output?
This is a more helpful error:
cyg ~$ cd /Users/adam/anaconda/envs/casa/lib/python2.7/site-packages/__casac__
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ python -c 'import _atmosphere'
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: dlopen(./_atmosphere.so, 2): Library not loaded: @rpath/libxml2.2.dylib
Referenced from: /Users/adam/anaconda/envs/casa/lib/libalma.47.0.0.dylib
Reason: Incompatible library version: libalma.47.0.0.dylib requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0
but it looks like I'm on the latest? =(
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ conda search libxml
Fetching package metadata .................
libxml2 2.9.0 0 defaults
2.9.0 1 defaults
2.9.2 0 defaults
2.9.4 0 defaults
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ conda search -c conda-forge -c pkgw-forge libxml
Fetching package metadata .....................
libxml2 2.9.0 0 defaults
2.9.0 1 defaults
2.9.2 0 defaults
2.9.4 0 defaults
2.9.3 6 conda-forge
2.9.3 7 conda-forge
2.9.3 8 conda-forge
2.9.3 9 conda-forge
2.9.4 0 conda-forge
2.9.4 1 conda-forge
2.9.4 2 conda-forge
2.9.4 3 conda-forge
* 2.9.4 4 conda-forge
libxmlpp 2.40.1 0 conda-forge
2.40.1 1 conda-forge
2.40.1 2 conda-forge
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ conda list | grep libxml
libxml2 2.9.4 4 conda-forge
Hmmm. It looks like the version of libxml2
provided by conda-forge
should have a compatibility version of 12.4.0 ... which leads me to suspect that for some reason the linker is finding a different version of the shared library installed elsewhere.
If you run otool -L ~/anaconda/envs/casa/lib/libxml2.2.dylib
, does the first line report that the "current version" is indeed 12.4.0?
yep:
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ otool -L ~/anaconda/envs/casa/lib/libxml2.2.dylib
/Users/adam/anaconda/envs/casa/lib/libxml2.2.dylib:
@rpath/libxml2.2.dylib (compatibility version 12.0.0, current version 12.4.0)
@rpath/libicui18n.58.dylib (compatibility version 58.0.0, current version 58.1.0)
@rpath/libicuuc.58.dylib (compatibility version 58.0.0, current version 58.1.0)
@rpath/libicudata.58.dylib (compatibility version 58.0.0, current version 58.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
@rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
@rpath/liblzma.5.dylib (compatibility version 8.0.0, current version 8.2.0)
@rpath/libiconv.2.dylib (compatibility version 8.0.0, current version 8.1.0)
How about running DYLD_PRINT_LIBRARIES=1 DYLD_PRINT_LIBRARIES_POST_LAUNCH=1 python -c "import _atmosphere"
from the __casac__
directory as above?
Excellent, that was the trick I was looking for - had no idea how to look for that stuff.
dyld: loaded: /Users/adam/anaconda/envs/casa/bin/python
dyld: loaded: /Users/adam/anaconda/envs/casa/bin/../lib//libpython2.7.dylib
dyld: loaded: /usr/lib/libSystem.B.dylib
dyld: loaded: /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
dyld: loaded: /usr/lib/system/libcache.dylib
dyld: loaded: /usr/lib/system/libcommonCrypto.dylib
dyld: loaded: /usr/lib/system/libcompiler_rt.dylib
dyld: loaded: /usr/lib/system/libcopyfile.dylib
dyld: loaded: /usr/lib/system/libcorecrypto.dylib
dyld: loaded: /usr/lib/system/libdispatch.dylib
dyld: loaded: /usr/lib/system/libdyld.dylib
dyld: loaded: /usr/lib/system/libkeymgr.dylib
dyld: loaded: /usr/lib/system/liblaunch.dylib
dyld: loaded: /usr/lib/system/libmacho.dylib
dyld: loaded: /usr/lib/system/libquarantine.dylib
dyld: loaded: /usr/lib/system/libremovefile.dylib
dyld: loaded: /usr/lib/system/libsystem_asl.dylib
dyld: loaded: /usr/lib/system/libsystem_blocks.dylib
dyld: loaded: /usr/lib/system/libsystem_c.dylib
dyld: loaded: /usr/lib/system/libsystem_configuration.dylib
dyld: loaded: /usr/lib/system/libsystem_dnssd.dylib
dyld: loaded: /usr/lib/system/libsystem_info.dylib
dyld: loaded: /usr/lib/system/libsystem_kernel.dylib
dyld: loaded: /usr/lib/system/libsystem_m.dylib
dyld: loaded: /usr/lib/system/libsystem_malloc.dylib
dyld: loaded: /usr/lib/system/libsystem_network.dylib
dyld: loaded: /usr/lib/system/libsystem_notify.dylib
dyld: loaded: /usr/lib/system/libsystem_platform.dylib
dyld: loaded: /usr/lib/system/libsystem_pthread.dylib
dyld: loaded: /usr/lib/system/libsystem_sandbox.dylib
dyld: loaded: /usr/lib/system/libsystem_stats.dylib
dyld: loaded: /usr/lib/system/libunc.dylib
dyld: loaded: /usr/lib/system/libunwind.dylib
dyld: loaded: /usr/lib/system/libxpc.dylib
dyld: loaded: /usr/lib/libobjc.A.dylib
dyld: loaded: /usr/lib/libauto.dylib
dyld: loaded: /usr/lib/libc++abi.dylib
dyld: loaded: /usr/lib/libc++.1.dylib
dyld: loaded: /usr/lib/libDiagnosticMessagesClient.dylib
dyld: loaded: /usr/lib/libicucore.A.dylib
dyld: loaded: /usr/lib/libz.1.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/python2.7/lib-dynload/_locale.so
dyld: loaded: ./_atmosphere.so
dyld: loaded: /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libgfortran.3.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libatnf.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libalma.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libatmosphere.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcalanalysis.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasadbus.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasaqt.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcomponents.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libdisplay.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libflagging.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libgraphics.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libimageanalysis.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libmiriad.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libmstransform.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libnrao.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libplotms.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libsingledish.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libspectrallines.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libstdcasa.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libsynthesis.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libasdmstman.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libmsvis.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_sakura.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libparallel.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_casa.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_coordinates.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_fits.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_images.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_lattices.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_measures.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_mirlib.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_ms.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_msfits.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_scimath.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_scimath_f.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcasa_tables.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libopenblasp-r0.2.19.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libcfitsio.5.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libwcs.5.16.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libpgsbox.5.16.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libpgplot.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libfftw3_threads.3.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libfftw3f_threads.3.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libfftw3f.3.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libfftw3.3.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libsakura.3.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libtools.47.0.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtCore.4.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtGui.4.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtDBus.4.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtXml.4.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libdbus-c++-1.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libreadline.6.2.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libncursesw.5.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libxerces-c.28.dylib
dyld: loaded: /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
dyld: loaded: /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
dyld: loaded: /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
dyld: loaded: /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
dyld: loaded: /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
dyld: loaded: /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
dyld: loaded: /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
dyld: loaded: /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
dyld: loaded: /System/Library/Frameworks/Security.framework/Versions/A/Security
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
dyld: loaded: /usr/lib/libxml2.2.dylib
dyld: loaded: /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
dyld: loaded: /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
dyld: loaded: /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
dyld: loaded: /usr/lib/liblangid.dylib
dyld: loaded: /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
dyld: loaded: /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
dyld: loaded: /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
dyld: loaded: /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/GenerationalStorage
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
dyld: loaded: /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
dyld: loaded: /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
dyld: loaded: /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
dyld: loaded: /System/Library/PrivateFrameworks/Backup.framework/Versions/A/Backup
dyld: loaded: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
dyld: loaded: /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
dyld: loaded: /usr/lib/libCRFSuite.dylib
dyld: loaded: /usr/lib/libbsm.0.dylib
dyld: loaded: /usr/lib/libsqlite3.dylib
dyld: loaded: /usr/lib/libxar.1.dylib
dyld: loaded: /usr/lib/libpam.2.dylib
dyld: loaded: /usr/lib/libOpenScriptingUtil.dylib
dyld: loaded: /usr/lib/libbz2.1.0.dylib
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
dyld: loaded: /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
dyld: loaded: /usr/lib/system/libkxld.dylib
dyld: loaded: /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
dyld: loaded: /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
dyld: loaded: /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement
dyld: loaded: /usr/lib/libxslt.1.dylib
dyld: loaded: /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
dyld: loaded: /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
dyld: loaded: /usr/lib/libcups.2.dylib
dyld: loaded: /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
dyld: loaded: /System/Library/Frameworks/GSS.framework/Versions/A/GSS
dyld: loaded: /usr/lib/libresolv.9.dylib
dyld: loaded: /usr/lib/libiconv.2.dylib
dyld: loaded: /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal
dyld: loaded: /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
dyld: loaded: /usr/lib/libheimdal-asn1.dylib
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
dyld: loaded: /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
dyld: loaded: /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
dyld: loaded: /System/Library/PrivateFrameworks/Bom.framework/Versions/A/Bom
dyld: loaded: /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
dyld: loaded: /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Versions/A/CoreImage
dyld: loaded: /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserInterface
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
dyld: loaded: /System/Library/PrivateFrameworks/FaceCore.framework/Versions/A/FaceCore
dyld: loaded: /System/Library/PrivateFrameworks/CrashReporterSupport.framework/Versions/A/CrashReporterSupport
dyld: loaded: /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
dyld: loaded: /System/Library/PrivateFrameworks/AppleFSCompression.framework/Versions/A/AppleFSCompression
dyld: loaded: /System/Library/PrivateFrameworks/Ubiquity.framework/Versions/A/Ubiquity
dyld: loaded: /System/Library/PrivateFrameworks/IconServices.framework/Versions/A/IconServices
dyld: loaded: /System/Library/PrivateFrameworks/ChunkingLibrary.framework/Versions/A/ChunkingLibrary
dyld: loaded: /System/Library/PrivateFrameworks/CoreSymbolication.framework/Versions/A/CoreSymbolication
dyld: loaded: /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
dyld: loaded: /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libquadmath.0.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libgcc_s.1.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_regex.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_program_options.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_filesystem.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_system.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_thread.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_chrono.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_date_time.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libboost_atomic.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/librpfits.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libhdf5.10.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libhdf5_hl.10.dylib
dyld: loaded: /usr/lib/libncurses.5.4.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libtinfow.5.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libicudata.58.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libicui18n.58.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libicuuc.58.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libpng16.16.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib/libX11.6.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libxcb.1.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libXau.6.dylib
dyld: loaded: /Users/adam/anaconda/envs/casa/lib//libXdmcp.6.dylib
dyld: unloaded: ./_atmosphere.so
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libgfortran.3.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libatnf.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libalma.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libatmosphere.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcalanalysis.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasadbus.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasaqt.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcomponents.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libdisplay.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libflagging.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libgraphics.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libimageanalysis.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libmiriad.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libmstransform.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libnrao.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libplotms.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libsingledish.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libspectrallines.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libstdcasa.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libsynthesis.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libasdmstman.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libmsvis.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_sakura.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libparallel.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_casa.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_coordinates.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_fits.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_images.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_lattices.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_measures.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_mirlib.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_ms.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_msfits.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_scimath.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_scimath_f.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcasa_tables.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libopenblasp-r0.2.19.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libcfitsio.5.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libwcs.5.16.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libpgsbox.5.16.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libpgplot.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libfftw3_threads.3.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libfftw3f_threads.3.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libfftw3f.3.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libfftw3.3.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libsakura.3.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libtools.47.0.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtCore.4.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtGui.4.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtDBus.4.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/../qt4/lib/libQtXml.4.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libdbus-c++-1.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libreadline.6.2.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libncursesw.5.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libxerces-c.28.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libquadmath.0.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libgcc_s.1.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_regex.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_program_options.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_filesystem.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_system.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_thread.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_chrono.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_date_time.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libboost_atomic.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/librpfits.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libhdf5.10.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libhdf5_hl.10.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libtinfow.5.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libicudata.58.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libicui18n.58.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libicuuc.58.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libpng16.16.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib/libX11.6.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libxcb.1.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libXau.6.dylib
dyld: unloaded: /Users/adam/anaconda/envs/casa/lib//libXdmcp.6.dylib
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: dlopen(./_atmosphere.so, 2): Library not loaded: @rpath/libxml2.2.dylib
Referenced from: /Users/adam/anaconda/envs/casa/lib/libalma.47.0.0.dylib
Reason: Incompatible library version: libalma.47.0.0.dylib requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0
Huh... it's taking /usr/lib/libxml...
instead of the conda one.
Looks like it's because of the DYLD_FALLBACK_LIBRARY_PATH
, unfortunately:
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ env | grep DYLD
DYLD_FALLBACK_LIBRARY_PATH=/Users/adam/anaconda/envs/astropy35/lib/:/usr/local/lib:/lib:/usr/lib
DYLD_LIBRARY_PATH=/usr/local/netpbm/lib/
that gets me to a different error:
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ DYLD_FALLBACK_LIBRARY_PATH="" DYLD_LIBRARY_PATH="" python -c 'import _atmosphere'
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: dlopen(./_atmosphere.so, 2): Library not loaded: /Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/libgcc_s.1.dylib
Referenced from: /Users/adam/anaconda/envs/casa/lib/libcasa_scimath_f.2.dylib
Reason: image not found
Ok. It should definitely be possible for Conda installs to work without needing to set the LIBRARY_PATH variables. Not clear to me why the scimath library is pulling in the weird gcc_s path - I've seen problems of that kind before but everything works for me right now. Will investigate further.
I think that a rebuild of the casacore
package in conda-forge
will fix this problem, although I may end up having to rebuild casa-tools
and/or casa-python
as well. Please upgrade and test when version 2.2.0_1
of casacore
becomes available on conda-forge
. That should take less than a day to happen, or so.
:+1: thanks
Yes, things are looking promising. When you have a chance, please let me know if the combination of the updated casacore
and getting rid of the LIBRARY_PATH
variables gets things to work.
My first attempt:
$ conda install -n casa -c conda-forge -c pkgw-forge casa-python casacore
Fetching package metadata .....................
Solving package specifications: .
Package plan for installation in environment /Users/adam/anaconda/envs/casa:
The following packages will be UPDATED:
casacore: 2.2.0-0 conda-forge --> 2.2.0-1 conda-forge
casacore-2.2.0 100% |#########################################################################################################################| Time: 0:00:01 7.33 MB/
did not work:
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ DYLD_FALLBACK_LIBRARY_PATH="" DYLD_LIBRARY_PATH="" python -c 'import _atmosphere'Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: dlopen(./_atmosphere.so, 2): Library not loaded: @rpath/libxml2.2.dylib
Referenced from: /Users/adam/anaconda/envs/casa/lib/libalma.47.0.0.dylib
Reason: Incompatible library version: libalma.47.0.0.dylib requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0
the problem is the same as before:
cyg ~/anaconda/envs/casa/lib/python2.7/site-packages/__casac__$ DYLD_FALLBACK_LIBRARY_PATH="" DYLD_LIBRARY_PATH="" DYLD_PRINT_LIBRARIES=1 DYLD_PRINT_LIBRARIES_POST_LAUNCH=1 python -c "import _atmosphere" 2>&1 | grep libxml
dyld: loaded: /usr/lib/libxml2.2.dylib
Do I need to uninstall & reinstall the whole stack, perhaps?
Hmmm, I don't think that an uninstall/reinstall will help.
It is strange to me that it's still picking up the system version of libxml2 when the LIBRARY_PATH
variables are cleared, at least given that clearing them seems to have made that problem go away before. I'll have to do some more digging.
What version of OSX are you on, by the way?
10.9.5
Hmmmm. I believe that conda-forge packages should still support 10.9, but that's not 100% clear to me (discussion). On my 10.12 system, /usr/lib/libxml2.dylib
still has a compatibility version of 10.0.0
, so if the mere presence of such a library caused problems, I should have issues too, and I don't.
I had LD_LIBRARY_PATH
set; I had to unset it to get the appropriate dylib to load.
Also, for reasons I cannot understand, ipython was loading my git version instead of the conda-installed version, so my final successful command was:
cyg ~$ env -i LD_LIBRARY_PATH="" DYLD_FALLBACK_LIBRARY_PATH="" DYLD_LIBRARY_PATH="" ~/anaconda/envs/casa/bin/ipython
In [1]: import casac
In [2]:
Thanks @pkgw!
(EDIT: note that the three environmental variables being set are redundant with env -i
on the line; that was added because of the weird ipython issue)
I installed
casa-python
with the commandconda install -n astropy27 -c conda-forge -c pkgw-forge casa-python=4.7.2
. However, on import, I get the following error:Does this imply I'm missing some dependency?