miniconda2 for mac issues: dlsym(RTLD_DEFAULT, AbsoluteToNanoseconds): symbol not found

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mingming ding

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Nov 14, 2020, 9:00:47 PM11/14/20
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Hi all,
Did someone experience this issue. Thanks a lot for help out.
BRS, BRUCE

# mingmingding @ MINGMINDING-MB0 in ~/miniconda2/envs on git:master x [9:23:34]
$ conda install AbsoluteToNanoseconds
Traceback (most recent call last):
  File "/Users/mingmingding/miniconda2/bin/conda", line 13, in <module>
    sys.exit(main())
  File "/Users/mingmingding/miniconda2/lib/python2.7/site-packages/conda/cli/main.py", line 149, in main
    from ..exceptions import conda_exception_handler
  File "/Users/mingmingding/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 19, in <module>
    from ._vendor.auxlib.entity import EntityEncoder
  File "/Users/mingmingding/miniconda2/lib/python2.7/site-packages/conda/_vendor/auxlib/entity.py", line 253, in <module>
    from .collection import AttrDict, frozendict, make_immutable
  File "/Users/mingmingding/miniconda2/lib/python2.7/site-packages/conda/_vendor/auxlib/collection.py", line 10, in <module>
    from .compat import isiterable, iteritems, odict, text_type
  File "/Users/mingmingding/miniconda2/lib/python2.7/site-packages/conda/_vendor/auxlib/compat.py", line 10, in <module>
    from ._vendor.five import WhateverIO as StringIO, with_metaclass
  File "/Users/mingmingding/miniconda2/lib/python2.7/site-packages/conda/_vendor/auxlib/_vendor/five.py", line 80, in <module>
    absolute_to_nanoseconds = CoreServices.AbsoluteToNanoseconds
  File "/Users/mingmingding/miniconda2/lib/python2.7/ctypes/__init__.py", line 379, in __getattr__
    func = self.__getitem__(name)
  File "/Users/mingmingding/miniconda2/lib/python2.7/ctypes/__init__.py", line 384, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: dlsym(RTLD_DEFAULT, AbsoluteToNanoseconds): symbol not found

Ray Donnelly

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Nov 15, 2020, 3:15:53 AM11/15/20
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Are you using Big Sur?

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Febby Chang

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Nov 15, 2020, 6:08:36 AM11/15/20
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Yes I am 

Sent from my iPhone

On Nov 15, 2020, at 3:15 AM, Ray Donnelly <rdon...@anaconda.com> wrote:



Ray Donnelly

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Nov 15, 2020, 6:22:23 AM11/15/20
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Can you try to reinstall from scratch. Someone reported that this worked for them.

Febby Chang

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Nov 15, 2020, 7:16:46 AM11/15/20
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I did try that however it would keep showing me that anaconda3 needs to update like it’s installed already. 

mingming ding

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Nov 15, 2020, 7:56:42 AM11/15/20
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please ignore this email. Resolved this issue by source ~/.zshrc.  I sitll donot know why :)

$ vim ~/.zshrc

# mingmingding @ MINGMINDING-MB0 in ~/anaconda2/bin on git:master x [20:52:37]
$ source  ~/.zshrc
(base) ➜  bin git:(master) ✗ pwd
/Users/mingmingding/anaconda2/bin
(base) ➜  bin git:(master) ✗ sudo conda list
# packages in environment at /Users/mingmingding/anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py38_0
alabaster                 0.7.12                     py_0
anaconda                  2020.07                  py38_0
anaconda-client           1.7.2                    py38_0
anaconda-navigator        1.9.12                   py38_0
anaconda-project          0.8.4                      py_0
applaunchservices         0.2.1                      py_0
appnope                   0.1.0                 py38_1001
appscript                 1.1.1            py38haf1e3a3_0
argh                      0.26.2                   py38_0
asn1crypto                1.3.0                    py38_1
astroid                   2.4.2                    py38_0
astropy                   4.0.1.post1      py38h01d97ff_1
atomicwrites              1.4.0                      py_0
attrs                     19.3.0                     py_0
autopep8                  1.5.3                      py_0
babel                     2.8.0                      py_0
backcall                  0.2.0                      py_0
backports                 1.0                        py_2
backports.functools_lru_cache 1.6.1                      py_0
backports.shutil_get_terminal_size 1.0.0                    py38_2
backports.tempfile        1.0                        py_1
backports.weakref         1.0.post1                  py_1
beautifulsoup4            4.9.1                    py38_0
bitarray                  1.4.0            py38haf1e3a3_0
bkcharts                  0.2                      py38_0
blas                      1.0                         mkl
bleach                    3.1.5                      py_0
blosc                     1.19.0               hab81aa3_0
bokeh                     2.1.1                    py38_0
boto                      2.49.0                   py38_0
bottleneck                1.3.2            py38hf1fa96c_1
brotlipy                  0.7.0           py38haf1e3a3_1000
bzip2                     1.0.8                h1de35cc_0
ca-certificates           2020.6.24                     0
certifi                   2020.6.20                py38_0
cffi                      1.14.0           py38hc512035_1
chardet                   3.0.4                 py38_1003
click                     7.1.2                      py_0
cloudpickle               1.5.0                      py_0
clyent                    1.2.2                    py38_1
colorama                  0.4.3                      py_0
conda                     4.8.3                    py38_0
conda-build               3.18.11                  py38_0
conda-env                 2.6.0                         1
conda-package-handling    1.6.1            py38h1de35cc_0
conda-verify              3.4.2                      py_1
contextlib2               0.6.0.post1                py_0
cryptography              2.9.2            py38ha12b0ac_0
curl                      7.71.1               hb0a8c7a_1
cycler                    0.10.0                   py38_0
cython                    0.29.21          py38hb1e8313_0
cytoolz                   0.10.1           py38h1de35cc_0
dask                      2.20.0                     py_0
dask-core                 2.20.0                     py_0
dbus                      1.13.16              h18a8e69_0
decorator                 4.4.2                      py_0
defusedxml                0.6.0                      py_0
diff-match-patch          20200713                   py_0
distributed               2.20.0                   py38_0
docutils                  0.16                     py38_1
entrypoints               0.3                      py38_0
et_xmlfile                1.0.1                   py_1001
expat                     2.2.9                hb1e8313_2
fastcache                 1.1.0            py38h1de35cc_0
filelock                  3.0.12                     py_0
flake8                    3.8.3                      py_0
flask                     1.1.2                      py_0
freetype                  2.10.2               ha233b18_0
fsspec                    0.7.4                      py_0
future                    0.18.2                   py38_1
get_terminal_size         1.0.0                h7520d66_0
gettext                   0.19.8.1             hb0f4f8b_2
gevent                    20.6.2           py38haf1e3a3_0
glib                      2.65.0               hc5f4afa_0
glob2                     0.7                        py_0
gmp                       6.1.2                hb37e062_1
gmpy2                     2.0.8            py38h6ef4df4_3
greenlet                  0.4.16           py38haf1e3a3_0
h5py                      2.10.0           py38h3134771_0
hdf5                      1.10.4               hfa1e0ec_0
heapdict                  1.0.1                      py_0
html5lib                  1.1                        py_0
icu                       58.2                 h0a44026_3
idna                      2.10                       py_0
imageio                   2.9.0                      py_0
imagesize                 1.2.0                      py_0
importlib-metadata        1.7.0                    py38_0
importlib_metadata        1.7.0                         0



Febby Chang

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Nov 15, 2020, 5:59:13 PM11/15/20
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Hi it still won't let me install it the same error is popping up it says "Anaconda3 is already installed in/opt/anaconda3. Use 'conda update anaconda3' to update Anaconda3." I have tried the other methods and I still can't get rid of it. 

Ray Donnelly

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Nov 15, 2020, 7:01:53 PM11/15/20
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Please move the old installation out of the way first. From Terminal:

mv /opt/anaconda3 /opt/anaconda3.old

.. then try again.

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Martin Kaspar

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Jan 19, 2021, 2:32:46 PM (8 days ago) Jan 19
to anac...@continuum.io, Martin Kaspar, Martin Kaspar
Hello dear Anaconda-experts,


since MX-Linux (see http:www.mxlinux.org) does not have added Anaconda to MX Repository Package all the many many folks on MX-linux (which is ranked as #1 Linux
( cf. http://www.distrowatch.com ) for years now - all the folks out there do hot have a good anaconda-support.


Thats a sad sad story.  Can you do anything and help the community. this would be great!

See the hacky - damned hackish solution: The Arch PKGBUILD has some links for the installer that they use to provide the source:
https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=anaconda

They say it’s open source, we need that to package it, unless we just provide a routine to the installer.

====================================

this is the link to the Archlinux-stuff: https://aur.archlinux.org/cgit/aur.git/tree/?h=anaconda

The Tree section shows us list of links like this, with the code behind each link

Mode Name Size
-rw-r--r-- .SRCINFO 627 logstatsplain
-rw-r--r-- .gitignore 43 logstatsplain
-rw-r--r-- PKGBUILD 1233 logstatsplain
-rw-r--r-- anaconda.install 219 logstatsplain

but honestly - i have never been doing installation based only on files - always

sudo apt-get install xyz

i bet such compiling is easy, when most of the job is already done - like here - if i would even once went trough the process like that - i would know what to do, but i have had not yet.
how i suppose to install anaconda based on those files?

he package() function in the PKGBUILD lists the install steps. $pkgdir is basically the local filesystem tree and $srcdir is the name of the directory from which the install script is run.

So to break it down:
CODE: SELECT ALL

sudo mkdir /opt
pkgname=anaconda
pkgver=2020.02
mkdir -p ~/builds/$pkgname && cd ~/builds/$pkgname
wget http://repo.continuum.io/archive/Anaconda3-${pkgver}-Linux-x86_64.sh
prefix=/opt/${pkgname}
LD_PRELOAD="/usr/lib/libfakeroot/libfakeroot.so"
sudo bash Anaconda3-${pkgver}-Linux-x86_64.sh -b -p $prefix -f
cd $prefix
sudo chmod a+r -R pkgs
sudo sed -e "s|/||g" -i $(grep "/" . -rIl 2>/dev/null)
And here are the instructions:
CODE: SELECT ALL

Please run

        $ source /opt/anaconda/bin/activate root
        $ source /opt/anaconda/bin/deactivate root

to activate and deactivate the anaconda enviroment.
The Anaconda software will be installed under /opt/anaconda with the build script in ~/builds/anaconda

Warning: This method is hacky in the extreme, it would probably be better to ask the MX devs to package the software properly instead.

so fine folks - plz help out - can you provide some support to the repo-manager of the mx-linux community.

remember - the mx-group is ranked as #1 Linux at distrowatch for years now.

love to hear  from you
regards martin   


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