Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
On 06/13/2018 01:10 PM, Greg Landrum wrote: > You don't excerpt the earlier message where I explained how to get things > working without needing X installed. Was that not clear? If you don't want > to have X installed but would still like to use the conda builds, you can > just install the two packages from the RDKit channel. There's more to it than that. Conda as packaged for a given distro has itself a set of dependencies. As I said before, *for example* installing conda on a centos 6 server will take it off the network at the next maintenance reboot, unless the installer knows they're doing and watches the whole ting very carefully. No, it's not your problem, you're doing the best you can, and thank you for that. But the end result is that ready-made builds are getting increasingly too bloated to be of use, and custom builds are too "non-trivial" to attempt. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
On Wed, Jun 13, 2018 at 5:51 PM Dimitri Maziuk via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > On 6/13/2018 10:06 AM, Greg Landrum wrote: > > Note that my answer assumes that there is a reason that you don't have > > X11 installed on your linux box. If that's not the case, you should be > > able to fix things "more easily" by installing X > > Quite frankly, this is rapidly becoming unusable as a software platform. > I need to install X11 to UUF-optimize a MOL? Seriously? > You don't excerpt the earlier message where I explained how to get things working without needing X installed. Was that not clear? If you don't want to have X installed but would still like to use the conda builds, you can just install the two packages from the RDKit channel. If you aren't using conda, none of this is relevant and you have to build the RDKit yourself anyway, as Geoff pointed out. We know that this is non-trivial for many people, and that's why we provide the conda builds. -greg > > E.g. on centos anaconda installs NetworkManager (why?) which comes in > "enabled at boot" but not configured, so next time you reboot, perhaps > weeks later, tada! -- you've lost the network. And don't get me started > on having several versions of boost coexist... > > Dima > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
On 06/13/2018 11:44 AM, Geoffrey Hutchison wrote: > > No, you can compile RDKit yourself if you don't want to use X11 features. You > wanted to install through conda, which has a set of packages for 'most use' - > YMMV. Sadly, MM does indeed V. On my box I can't, not without also compiling boost myself -- and I haven't looked further. Wouldn't be surprised if it takes me all the way to compiling GNU Compiler Collection myself too. Some day I'll get a round tuit to set up an alpine build VM and see if it compiles there... so I can roll it into a reasonable-sized docker container, but compiling it on my desktop is simply not worth my time. (And our compute nodes are the same or older as my desktop, so if it doesn't work on my box, we can't deploy it anywhere.) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
Great! -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e Inteligência Computacional - UNIFEI Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG Em qua, 13 de jun de 2018 às 13:45, Geoffrey Hutchison < geoff.hutchi...@gmail.com> escreveu: > >> Note that my answer assumes that there is a reason that you don't have > X11 installed on your linux box. If that's not the case, you should be able > to fix things "more easily" by installing X > > > > Quite frankly, this is rapidly becoming unusable as a software platform. > I need to install X11 to UUF-optimize a MOL? Seriously? > > No, you can compile RDKit yourself if you don't want to use X11 features. > You wanted to install through conda, which has a set of packages for 'most > use' - YMMV. > (We have a version of RDKit on our server w/o X11) > > My $0.02, > -Geoff > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
>> Note that my answer assumes that there is a reason that you don't have X11 >> installed on your linux box. If that's not the case, you should be able to >> fix things "more easily" by installing X > > Quite frankly, this is rapidly becoming unusable as a software platform. I > need to install X11 to UUF-optimize a MOL? Seriously? No, you can compile RDKit yourself if you don't want to use X11 features. You wanted to install through conda, which has a set of packages for 'most use' - YMMV. (We have a version of RDKit on our server w/o X11) My $0.02, -Geoff -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
Just run sudo apt-get install libxrender1 and it works Chris Earnshaw has send me a email with this tip. Thanks!!! -- Wandré Nunes de Pinho Veloso Professor Assistente - Unifei - Campus Avançado de Itabira-MG Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e Inteligência Computacional - UNIFEI Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG Em qua, 13 de jun de 2018 às 12:51, Dimitri Maziuk via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> escreveu: > On 6/13/2018 10:06 AM, Greg Landrum wrote: > > Note that my answer assumes that there is a reason that you don't have > > X11 installed on your linux box. If that's not the case, you should be > > able to fix things "more easily" by installing X > > Quite frankly, this is rapidly becoming unusable as a software platform. > I need to install X11 to UUF-optimize a MOL? Seriously? > > E.g. on centos anaconda installs NetworkManager (why?) which comes in > "enabled at boot" but not configured, so next time you reboot, perhaps > weeks later, tada! -- you've lost the network. And don't get me started > on having several versions of boost coexist... > > Dima > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
On 6/13/2018 10:06 AM, Greg Landrum wrote: Note that my answer assumes that there is a reason that you don't have X11 installed on your linux box. If that's not the case, you should be able to fix things "more easily" by installing X Quite frankly, this is rapidly becoming unusable as a software platform. I need to install X11 to UUF-optimize a MOL? Seriously? E.g. on centos anaconda installs NetworkManager (why?) which comes in "enabled at boot" but not configured, so next time you reboot, perhaps weeks later, tada! -- you've lost the network. And don't get me started on having several versions of boost coexist... Dima -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
Note that my answer assumes that there is a reason that you don't have X11 installed on your linux box. If that's not the case, you should be able to fix things "more easily" by installing X On Wed, Jun 13, 2018 at 5:05 PM Greg Landrum wrote: > Hi, > > This looks like an error caused by the fact that the anaconda cairo builds > include a dependency on the system X libraries and you don't have X > installed. > You can probably clear the problem up by installing the cairo build from > the RDKit channel. Run this inside the conda environment where you have the > RDKit installed: > > conda install -c rdkit nox > conda install -c rdkit cairo > > -greg > > > > On Wed, Jun 13, 2018 at 3:14 PM Wandré wrote: > >> Hi all! >> >> I install the Anaconda 4.5.4 with Python 3.6.5 and install rdkit (with >> command "conda install -c rdkit rdkit") and I'm trying to import the Chem >> and does not works. >> >> from rdkit import Chem >> >> Traceback (most recent call last): >> >> File "", line 1, in >> >> File >> "/home/wandre/anaconda3/envs/flaskapp/lib/python3.6/site-packages/rdkit/Chem/__init__.py", >> line 25, in >> >> from rdkit.Chem.rdmolops import * >> >> ImportError: libXrender.so.1: cannot open shared object file: No such >> file or directory >> >> How can I fix this? Where is my error? >> >> Thanks! >> -- >> Wandré Nunes de Pinho Veloso >> Professor Assistente - Unifei - Campus Avançado de Itabira-MG >> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG >> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e >> Inteligência Computacional - UNIFEI >> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ >> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG >> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't import Chem from rdkit in Anaconda Python 3.6.5
Hi, This looks like an error caused by the fact that the anaconda cairo builds include a dependency on the system X libraries and you don't have X installed. You can probably clear the problem up by installing the cairo build from the RDKit channel. Run this inside the conda environment where you have the RDKit installed: conda install -c rdkit nox conda install -c rdkit cairo -greg On Wed, Jun 13, 2018 at 3:14 PM Wandré wrote: > Hi all! > > I install the Anaconda 4.5.4 with Python 3.6.5 and install rdkit (with > command "conda install -c rdkit rdkit") and I'm trying to import the Chem > and does not works. > > from rdkit import Chem > > Traceback (most recent call last): > > File "", line 1, in > > File > "/home/wandre/anaconda3/envs/flaskapp/lib/python3.6/site-packages/rdkit/Chem/__init__.py", > line 25, in > > from rdkit.Chem.rdmolops import * > > ImportError: libXrender.so.1: cannot open shared object file: No such file > or directory > > How can I fix this? Where is my error? > > Thanks! > -- > Wandré Nunes de Pinho Veloso > Professor Assistente - Unifei - Campus Avançado de Itabira-MG > Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG > Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e > Inteligência Computacional - UNIFEI > Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ > Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG > Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
