clean install of conda python 3.7 rdkit rdkit for postgres on ubuntu 18.04 has boost version issues

[dpwildboar]

demonstration of issue

psql --port=15432 my-rdkit-db
psql (11.2)
Type "help" for help.

my-rdkit-db=# create extension rdkit;
ERROR: could not load library "/home/username/anaconda3/envs/my-rdkit/lib/rdkit.so": libboost_regex.so.1.65.1: cannot open shared object file: No such file or directory

versions of relevant things:

conda --version
conda 4.7.10

python --version
Python 3.7.3

uname -a
Linux iapetus 4.15.0-55-generic rdkit/rdkit#60-Ubuntu SMP Tue Jul 2 18:22:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

boost is installed however a more recent version:

cd ~/anaconda3/envs/my-rdkit/lib
ls libboost_regex.so*
libboost_regex.so libboost_regex.so.1.67.0

this workaround worked several weeks ago on another clean install.

try installing a prior version:

conda install -y boost=1.65.1 py-boost=1.65.1

Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
Initial quick solve with frozen env failed. Unfreezing env and trying again.
Solving environment: failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

• boost=1.65.1 -> python[version='>=2.7,<2.8.0a0,>=3.6,<3.7.0a0']
• py-boost=1.65.1 -> python[version='>=2.7,<2.8.0a0,>=3.6,<3.7.0a0']

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Your current python version
is (python=3.7). Note that conda will not change your python version to a different minor version
unless you explicitly specify that.

The following specifications were found to be incompatible with each other:

Package setuptools conflicts for:

snip

a masive list of stuff **

[greglandrum]

This is a bug related to the rdkit-conda packaging, not the RDKit.
Please report future bugs of this type here:
https://github.com/rdkit/conda-rdkit

[niraito]

I also have an unsatisfiable error 😞 were you able to solve it @dpwildboar, if so how???

Here is my command and output:

(base) root@LAPTOP-CF6MR4EE:~# conda install -c rdkit rdkit
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - rdkit -> python[version='2.6.*|2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|3.4.*']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:|@/linux-64::__glibc==2.31=0
  - rdkit -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

I see a bunch of similar issues on the web. But I am new at using the Ubuntu app on Windows 10, and various versions of python and R. While trying to correct my python version, I already crashed a lot of things and I have a lot of missing packages. Somehow I made it to a working python version 3.9.5, and I don't want to lose it again. So I wanted to ask the professionals here 😁

Here is the information of possibly related things' versions:

conda --version
conda 4.10.3

python --version
Python 3.9.5

uname -a
Linux LAPTOP-CF6MR4EE 4.4.0-19041-Microsoft #1237-Microsoft Sat Sep 11 14:32:00 PST 2021 x86_64 x86_64 x86_64 GNU/Linux

I hope I will be able to install RDKit at the end. Thanks in advance!!! 😊🙏🏻

[greglandrum]

Please install the rdkit from conda-forge, not the RDKit channel. We are no longer keeping the release builds on the rdkit channel up to date.

[niraito]

Okay, it worked! Thank you very much! 😊🙏🏻

[dpwildboar]

Greg is the Postgres rdkit install moving to forge also?

…

On Oct 1, 2021, at 7:58 AM, Greg Landrum ***@***.***> wrote: Please install the rdkit from conda-forge, not the RDKit channel. We are no longer keeping the release builds on the rdkit channel up to date. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACTCGYKMAVWCP5ZUS45HCLUEXEATANCNFSM4IJSF6JQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[greglandrum]

not yet, and unfortunately I haven't been particularly good about keeping those builds up-to-date either