So I'm certainly fine with a conda-forge only option, I don't happen to use
the rdkit channel version.
But I'll point out that I'm in the minority: comparing downloads of recent
versions on https://anaconda.org/rdkit/rdkit/files vs
https://anaconda.org/conda-forge/rdkit/files shows that the rdkit channel
is definitely used more frequently.
One concern: on a mac when I uninstall rdkit from the rdkit channel and
subsequently do a `conda install -c conda-forge rdkit`, I'll get a
non-working rdkit installation. I.e., >>> import rdkit.Chem throws a
SegFault.
That also appears to happen if you run conda create -n rdkit_test
conda-forge::rdkit. (see attachment)
So it appears that for the time being, mac conda-forge builds are going to
be best done as fresh installs with a bunch of the added conda-forge
dependencies:
$ conda create -n rdkit_test -c conda-forge rdkit
The following NEW packages will be INSTALLED:
blas: 1.0-mkl
boost: 1.68.0-py36h3e44d54_1 conda-forge
boost-cpp: 1.68.0-h3a22d5f_0 conda-forge
bzip2: 1.0.6-1 conda-forge
ca-certificates: 2018.10.15-ha4d7672_0 conda-forge
cairo: 1.14.12-h276e583_5 conda-forge
certifi: 2018.10.15-py36_1000 conda-forge
clangdev: 6.0.1-default_1 conda-forge
fontconfig: 2.13.1-hce039c3_0 conda-forge
freetype: 2.9.1-h6debe1e_4 conda-forge
gettext: 0.19.8.1-h1f1d5ed_1 conda-forge
glib: 2.56.2-h464dc38_0 conda-forge
icu: 58.2-hfc679d8_0 conda-forge
intel-openmp: 2019.0-118
jpeg: 9c-h470a237_1 conda-forge
libcxx: 6.0.1-0 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgfortran: 3.0.1-h93005f0_2
libiconv: 1.15-h470a237_3 conda-forge
libpng: 1.6.35-ha92aebf_2 conda-forge
libtiff: 4.0.9-he6b73bb_2 conda-forge
libxml2: 2.9.8-h422b904_5 conda-forge
llvm-meta: 6.0.1-0 conda-forge
llvmdev: 6.0.1-h2d50403_2 conda-forge
mkl: 2019.0-118
mkl_fft: 1.0.6-py36_0 conda-forge
mkl_random: 1.0.1-py36_0 conda-forge
ncurses: 6.1-hfc679d8_1 conda-forge
numpy: 1.15.2-py36h6a91979_1
numpy-base: 1.15.2-py36h8a80b8c_1
olefile: 0.46-py_0 conda-forge
openssl: 1.0.2p-h470a237_1 conda-forge
pandas: 0.23.4-py36hf8a1672_0 conda-forge
pcre: 8.41-hfc679d8_3 conda-forge
pillow: 5.3.0-py36hc736899_0 conda-forge
pip: 18.1-py36_1000 conda-forge
pixman: 0.34.0-h470a237_3 conda-forge
pycairo: 1.17.1-py36h4d1f301_0 conda-forge
python: 3.6.6-h5001a0f_0 conda-forge
python-dateutil: 2.7.3-py_0 conda-forge
pytz: 2018.5-py_0 conda-forge
rdkit: 2018.03.4-py36h557c172_1000 conda-forge
readline: 7.0-haf1bffa_1 conda-forge
setuptools: 40.4.3-py36_0 conda-forge
six: 1.11.0-py36_1001 conda-forge
sqlite: 3.25.2-hb1c47c0_0 conda-forge
tk: 8.6.8-ha92aebf_0 conda-forge
wheel: 0.32.1-py36_0 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
-- Peter
On Thu, Oct 18, 2018 at 11:02 AM Thomas Holder <
[email protected]> wrote:
> Note that it makes a difference whether you do "conda install -c
> conda-forge rdkit" or "conda install conda-forge::rdkit". The latter
> will pull in less packages from conda-forge.
>
> I'm on Linux, using a somewhat recent environment which has mostly
> default channel packages + rdkit::rdkit + openbabel::openbabel +
> schrodinger::pymol. This is what I get:
>
>
> ------------------------------------------------------------------------------
> $ conda install conda-forge::rdkit
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> boost-cpp-1.66.0 | 1 18.8 MB
> conda-forge
> boost-1.66.0 | py36_1 317 KB
> conda-forge
> pycairo-1.15.4 | py36h1b9232e_1 67 KB
> rdkit-2018.03.4 | py36ha4bbe77_0 19.4 MB
> conda-forge
> ------------------------------------------------------------
> Total: 38.5 MB
>
> The following NEW packages will be INSTALLED:
>
> boost: 1.66.0-py36_1 conda-forge
> boost-cpp: 1.66.0-1 conda-forge
> pycairo: 1.15.4-py36h1b9232e_1
>
> The following packages will be DOWNGRADED:
>
> rdkit: 2018.03.4.0-py36h71b666b_1 rdkit -->
> 2018.03.4-py36ha4bbe77_0 conda-forge
>
>
> ------------------------------------------------------------------------------
> $ conda install -c conda-forge rdkit
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> ca-certificates-2018.10.15 | ha4d7672_0 135 KB
> conda-forge
> certifi-2018.10.15 | py36_1000 138 KB
> conda-forge
> pycairo-1.17.1 | py36h4d1f301_0 202 KB
> conda-forge
> boost-cpp-1.66.0 | 1 18.8 MB
> conda-forge
> openssl-1.0.2p | h470a237_1 3.1 MB
> conda-forge
> boost-1.66.0 | py36_1 317 KB
> conda-forge
> rdkit-2018.03.4 | py36ha4bbe77_0 19.4 MB
> conda-forge
> ------------------------------------------------------------
> Total: 42.0 MB
>
> The following NEW packages will be INSTALLED:
>
> boost: 1.66.0-py36_1 conda-forge
> boost-cpp: 1.66.0-1 conda-forge
> pycairo: 1.17.1-py36h4d1f301_0 conda-forge
>
> The following packages will be UPDATED:
>
> ca-certificates: 2018.03.07-0 -->
> 2018.10.15-ha4d7672_0 conda-forge
> certifi: 2018.10.15-py36_0 -->
> 2018.10.15-py36_1000 conda-forge
> openssl: 1.0.2p-h14c3975_0 -->
> 1.0.2p-h470a237_1 conda-forge
>
> The following packages will be DOWNGRADED:
>
> rdkit: 2018.03.4.0-py36h71b666b_1 rdkit -->
> 2018.03.4-py36ha4bbe77_0 conda-forge
>
>
> ------------------------------------------------------------------------------
>
> Cheers,
> Thomas
>
> On Thu, Oct 18, 2018 at 4:43 PM Greg Landrum <[email protected]>
> wrote:
> >
> >
> >
> > On Thu, Oct 18, 2018 at 2:21 PM Eric Jonas <[email protected]> wrote:
> >>
> >> Greg, I'm all for anything that makes the release process on developers
> easier; my main question is : With conda-forge, how hard is it to install
> just _one_ package without having everything else (say numpy, pandas, etc)
> upgraded to the latest conda-forge version? I've had situations in the past
> where i'm like "oh I'd just like the latest ___" and suddenly everything in
> my conda env has been upgraded to the bleeding edge.
> >
> >
> > That's a great question, and it's one I don't really know the answer to.
> >
> > On my PC (I'm on the train, and this is what I have with me), here's
> what I did:
> > - create a new conda environment that includes an rdkit-channel RDKit
> install
> > - uninstall the RDKit from that
> > - install the RDKit from the conda-forge channel
> >
> > Here's what ends up getting changed:
> >
> > ## Package Plan ##
> >
> > environment location: C:\Users\glandrum\Anaconda3\envs\py36_tmp
> >
> > added / updated specs:
> > - rdkit
> >
> >
> > The following NEW packages will be INSTALLED:
> >
> > boost: 1.67.0-py36_vc14_0 conda-forge [vc14]
> > boost-cpp: 1.67.0-vc14_0 conda-forge [vc14]
> > pycairo: 1.16.3-py36_vc14_0 conda-forge [vc14]
> > rdkit: 2018.03.4-py36h857267b_1000 conda-forge
> >
> > The following packages will be UPDATED:
> >
> > certifi: 2018.10.15-py36_0 -->
> 2018.10.15-py36_1000 conda-forge
> > jpeg: 9b-hb83a4c4_2 --> 9b-vc14_2
> conda-forge [vc14]
> > tk: 8.6.8-hfa6e2cd_0 --> 8.6.8-vc14_0
> conda-forge [vc14]
> >
> > The following packages will be DOWNGRADED:
> >
> > icu: 58.2-ha66f8fd_1 --> 58.2-vc14_0
> conda-forge [vc14]
> > libpng: 1.6.35-h2a8f88b_0 -->
> 1.6.34-vc14_0 conda-forge [vc14]
> > libtiff: 4.0.9-h36446d0_2 --> 4.0.9-vc14_0
> conda-forge [vc14]
> > pillow: 5.3.0-py36hdc69c19_0 -->
> 5.2.0-py36h08bbbbd_0
> > pixman: 0.34.0-hcef7cb0_3 -->
> 0.34.0-vc14_2 conda-forge [vc14]
> > vc: 14.1-h0510ff6_4 --> 14-0
> conda-forge
> > zlib: 1.2.11-h8395fce_2 -->
> 1.2.11-vc14_0 conda-forge [vc14]
> >
> >
> > That's a fair amount of change, but is less than what I thought might
> happen (I was worried about numpy+pandas+... being updated).
> > So that's one data point. What's your take?
> >
> >
> > I will try the same thing on my Mac and Linux boxes tomorrow if no one
> else has done it by then.
> >
> > -greg
> >
> >
> > _______________________________________________
> > Rdkit-discuss mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
$ conda create -n rdkit-test -c rdkit rdkit
The following NEW packages will be INSTALLED:
blas: 1.0-mkl
bzip2: 1.0.6-h1de35cc_5
ca-certificates: 2018.03.07-0
cairo: 1.14.12-hc4e6be7_4
certifi: 2018.10.15-py36_0
fontconfig: 2.13.0-h5d5b041_1
freetype: 2.9.1-hb4e5f40_0
gettext: 0.19.8.1-h15daf44_3
glib: 2.56.2-hd9629dc_0
icu: 58.2-h4b95b61_1
intel-openmp: 2019.0-118
jpeg: 9b-he5867d9_2
libboost: 1.65.1-hcc95346_4
libcxx: 4.0.1-h579ed51_0
libcxxabi: 4.0.1-hebd6815_0
libedit: 3.1-hb4e282d_0
libffi: 3.2.1-h475c297_4
libgfortran: 3.0.1-h93005f0_2
libiconv: 1.15-hdd342a3_7
libpng: 1.6.35-ha441bb4_0
libtiff: 4.0.9-hcb84e12_2
libxml2: 2.9.8-hab757c2_1
mkl: 2019.0-118
mkl_fft: 1.0.6-py36hb8a8100_0
mkl_random: 1.0.1-py36h5d10147_1
ncurses: 6.0-0 rdkit
numpy: 1.15.2-py36h6a91979_1
numpy-base: 1.15.2-py36h8a80b8c_1
olefile: 0.46-py36_0
openssl: 1.0.2p-h1de35cc_0
pandas: 0.23.4-py36h6440ff4_0
pcre: 8.42-h378b8a2_0
pillow: 5.3.0-py36hb68e598_0
pip: 10.0.1-py36_0
pixman: 0.34.0-hca0a616_3
py-boost: 1.65.1-py36h1439ea1_4
python: 3.6.5-hc167b69_1
python-dateutil: 2.7.3-py36_0
pytz: 2018.5-py36_0
rdkit: 2018.03.4.0-py36h6adbef8_1 rdkit
readline: 7.0-hc1231fa_4
setuptools: 40.4.3-py36_0
six: 1.11.0-py36_1
sqlite: 3.23.1-hf1716c9_0
tk: 8.6.8-ha441bb4_0
wheel: 0.32.1-py36_0
xz: 5.2.4-h1de35cc_4
zlib: 1.2.11-hf3cbc9b_2
$ source activate rdkit-test
$ conda uninstall rdkit
$ conda install -c conda-forge rdkit
The following NEW packages will be INSTALLED:
boost: 1.68.0-py36h3e44d54_1 conda-forge
boost-cpp: 1.68.0-h3a22d5f_0 conda-forge
pycairo: 1.17.1-py36h4d1f301_0 conda-forge
rdkit: 2018.03.4-py36h557c172_1000 conda-forge
The following packages will be UPDATED:
ca-certificates: 2018.03.07-0 -->
2018.10.15-ha4d7672_0 conda-forge
certifi: 2018.10.15-py36_0 -->
2018.10.15-py36_1000 conda-forge
openssl: 1.0.2p-h1de35cc_0 -->
1.0.2p-h470a237_1 conda-forge
$ python
Python 3.6.5 |Anaconda, Inc.| (default, Apr 26 2018, 08:42:37)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit.Chem
[1] 90589 segmentation fault python
# Intalling via conda-forge
$ conda create -n rdkit_test conda-forge::rdkit
The following NEW packages will be INSTALLED:
blas: 1.0-mkl
boost: 1.67.0-py37_4
bzip2: 1.0.6-h1de35cc_5
ca-certificates: 2018.03.07-0
cairo: 1.14.12-hc4e6be7_4
certifi: 2018.10.15-py37_0
fontconfig: 2.13.0-h5d5b041_1
freetype: 2.9.1-hb4e5f40_0
gettext: 0.19.8.1-h15daf44_3
glib: 2.56.2-hd9629dc_0
icu: 58.2-h4b95b61_1
intel-openmp: 2019.0-118
jpeg: 9b-he5867d9_2
libboost: 1.67.0-hebc422b_4
libcxx: 4.0.1-h579ed51_0
libcxxabi: 4.0.1-hebd6815_0
libedit: 3.1.20170329-hb402a30_2
libffi: 3.2.1-h475c297_4
libgfortran: 3.0.1-h93005f0_2
libiconv: 1.15-hdd342a3_7
libpng: 1.6.35-ha441bb4_0
libtiff: 4.0.9-hcb84e12_2
libxml2: 2.9.8-hab757c2_1
mkl: 2019.0-118
mkl_fft: 1.0.6-py37hb8a8100_0
mkl_random: 1.0.1-py37h5d10147_1
ncurses: 6.1-h0a44026_0
numpy: 1.15.2-py37h6a91979_1
numpy-base: 1.15.2-py37h8a80b8c_1
olefile: 0.46-py37_0
openssl: 1.0.2p-h1de35cc_0
pandas: 0.23.4-py37h6440ff4_0
pcre: 8.42-h378b8a2_0
pillow: 5.3.0-py37hb68e598_0
pip: 10.0.1-py37_0
pixman: 0.34.0-hca0a616_3
py-boost: 1.67.0-py37h6440ff4_4
pycairo: 1.17.1-py37ha54c0a8_0
python: 3.7.0-hc167b69_0
python-dateutil: 2.7.3-py37_0
pytz: 2018.5-py37_0
rdkit: 2018.03.4-py37h557c172_1000 conda-forge
readline: 7.0-h1de35cc_5
setuptools: 40.4.3-py37_0
six: 1.11.0-py37_1
sqlite: 3.25.2-ha441bb4_0
tk: 8.6.8-ha441bb4_0
wheel: 0.32.1-py37_0
xz: 5.2.4-h1de35cc_4
zlib: 1.2.11-hf3cbc9b_2
$ python
Python 3.7.0 (default, Jun 28 2018, 07:39:16)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit.Chem
[1] 91008 segmentation fault python
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