Many thanks to everyone who contributed to this thread. The conclusion that I'm going to take from this is that, at the moment, it's probably best if I keep doing the RDKit builds and distributing them via the rdkit conda channel. I'll keep an eye on things and maybe we can reconsider this decision for the 2019.03 release.
Best, -greg On Fri, Oct 19, 2018 at 1:17 PM Matthew Swain via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > I think this demonstrates one drawback of conda-forge right now: it's best > to go 'all in' on conda-forge for all packages or you run the risk of a > broken environment. > > In this Mac example, I think the issue may just be due to minor > discrepancies between the recipes on the conda-forge and rdkit channels, so > it would hopefully just be a short-term problem while people transition and > the rdkit channel is phased out. > > However, on linux, conda-forge currently uses older compilers than the > defaults channel, so there may be ongoing issues with mixing conda-forge > and defaults packages. They are currently migrating the entire conda-forge > ecosystem to the new compilers (RDKit packages are actually already done, > hidden under the "gcc7" label, waiting to be activated when all other > packages are ready) so this will hopefully be resolved soon too. > > To use conda-forge for the time being, I'd actually recommend adding > conda-forge as the highest priority channel in your config (conda config > --add channels conda-forge) and then install into a clean environment (e.g. > conda create -n rdenv rdkit). But once the compiler migration is complete, > I'd hope that it would be relatively safe to install with "conda install -c > conda-forge rdkit" into an existing environment with other packages from a > mix of different channels. > > Matt > > On Oct 18, 2018, at 06:41 PM, "Peter St. John" <peterc.stj...@gmail.com> > wrote: > > 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 < > thomas.hol...@schrodinger.com> 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 <greg.land...@gmail.com> >> wrote: >> > >> > >> > >> > On Thu, Oct 18, 2018 at 2:21 PM Eric Jonas <jo...@ericjonas.com> 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 >> > Rdkit-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > Content-Type: text/plain; charset="us-ascii" > MIME-Version: 1.0 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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