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

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:

To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/anaconda/CAF5kcVWmE127mJ88rxPdDP2oA1R-gjqVZyqbLH6VCZoipHeFDw%40mail.gmail.com.

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.

To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/anaconda/FCD94A00-EA2D-4CA1-91A4-3AAC28CA5EB7%40gmail.com.

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.

To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/anaconda/CAF5kcVXkb6JmP_3eYb_aJ17Qn0GXb0FeDy7zeb9UovWhFHj5Vg%40mail.gmail.com.

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 PM1/19/21

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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