pkgw / conda-recipes

Miscellaneous "recipes" for the Conda packaging system.
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casac import error after successful install #2

Closed keflavich closed 7 years ago

keflavich commented 7 years ago

I installed casa-python with the command conda install -n astropy27 -c conda-forge -c pkgw-forge casa-python=4.7.2. However, on import, I get the following error:

$ ~/anaconda/envs/astropy27/bin/python -c "import casac"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/adam/anaconda/envs/astropy27/lib/python2.7/site-packages/casac.py", line 1, in <module>
    import __casac__
  File "/Users/adam/anaconda/envs/astropy27/lib/python2.7/site-packages/__casac__/__init__.py", line 51, in <module>
    from . import atmosphere
  File "/Users/adam/anaconda/envs/astropy27/lib/python2.7/site-packages/__casac__/atmosphere.py", line 17, in <module>
    _atmosphere = swig_import_helper()
  File "/Users/adam/anaconda/envs/astropy27/lib/python2.7/site-packages/__casac__/atmosphere.py", line 16, in swig_import_helper
    return importlib.import_module('_atmosphere')
  File "/Users/adam/anaconda/envs/astropy27/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named _atmosphere

Does this imply I'm missing some dependency?

pkgw commented 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?

keflavich commented 7 years ago

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
pkgw commented 7 years ago

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.

keflavich commented 7 years ago

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
pkgw commented 7 years ago

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?

keflavich commented 7 years ago

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
keflavich commented 7 years ago

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
pkgw commented 7 years ago

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?

keflavich commented 7 years ago

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)
pkgw commented 7 years ago

How about running DYLD_PRINT_LIBRARIES=1 DYLD_PRINT_LIBRARIES_POST_LAUNCH=1 python -c "import _atmosphere" from the __casac__ directory as above?

keflavich commented 7 years ago

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
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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
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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
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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
keflavich commented 7 years ago

Huh... it's taking /usr/lib/libxml... instead of the conda one.

keflavich commented 7 years ago

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
pkgw commented 7 years ago

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.

pkgw commented 7 years ago

CC scipy#59, casacore-feedstock#3.

pkgw commented 7 years ago

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.

keflavich commented 7 years ago

:+1: thanks

pkgw commented 7 years ago

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.

keflavich commented 7 years ago

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?

pkgw commented 7 years ago

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?

keflavich commented 7 years ago

10.9.5

pkgw commented 7 years ago

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.

keflavich commented 7 years ago

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)