Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

[Thomas Girke]

Awesome, thanks!

On Tue, Mar 16, 2021 at 11:40 PM Hervé Pagès 
wrote:

> Hi Thomas, Kevin,
>
> openbabel3 is now on malbec1 (Ubuntu 18.04). Kevin's
> ubuntu_18.04_openbabel3_debs.tar.gz worked like a charm. Thanks for
> making it so easy.
>
> Note that this addition will affect ChemmineOB build/check results on
> malbec1 on Thursday only:
>
>
>
> https://bioconductor.org/checkResults/3.12/bioc-LATEST/ChemmineOB/malbec1-install.html
>
> Cheers,
> H.
>
>
> On 3/16/21 10:24 AM, Hervé Pagès wrote:
> > @Kevin: Thanks for providing openbabel3 for Ubuntu 18.04. Will take a
> > look ASAP.
> >
> > @Thomas: Yes, the Ubuntu 18.04 builds are only used for the BioC 3.12
> > builds (release). BioC 3.13 and further BioC releases are/will be using
> > Ubuntu >= 20.04.
> >
> > Best,
> > H.
> >
> >
> > On 3/15/21 1:59 PM, Thomas Girke wrote:
> >> Thanks Hervé for your help with this.
> >>
> >> Kevin has provided the *.deb package for installing OpenBabel 3.x on
> >> Ubuntu 18.04. Just in case, below is how we usually install OpenBabel
> >> 3.x.x across different Ubuntu/Debian systems.
> >>
> >> BTW: is it correct to assume that the Ubuntu 18.04 builds will be
> >> discontinued in the next release in April?
> >>
> >> Thanks,
> >>
> >> Thomas
> >>
> >>
> >> ## Install ChemmineOB with OpenBabel 3.x from source
> >>
> >> ## First uninstall libopenbabel-dev (which is version 2.x.x) if
> >> already installed via
> >> sudo apt-get remove libopenbabel-dev; sudo apt-get purge
> >> libopenbabel-dev; sudo apt-get --purge autoremove libopenbabel-dev
> >> ## Some dependencies to install
> >> sudo apt install cmake libeigen3-dev libboost-all-dev
> >> ## Clone OpenBabel 3.x.x from GitHub here:
> >> https://github.com/openbabel/openbabel
> >> 
> >> git clone g...@github.com:openbabel/openbabel.git
> >> mkdir build; cd build
> >> cmake ../openbabel
> >> make
> >> sudo make install
> >> ## Install ChemmineOB where you provide environment variables
> >> including header files and ChemmineOB package iprovided as *.tar.gz
> >> (adjust paths if not correct)
> >> R CMD INSTALL
> >>
> --configure-args='--with-openbabel-include=/usr/local/include/openbabel3/
> >> --with-openbabel-lib=/usr/local/lib/openbabel/3.1.1'
> >> ChemmineOB_1.28.0.tar.gz
> >>
> >> On Mon, Mar 15, 2021 at 1:12 PM Kevin Horan  >> > wrote:
> >>
> >> Herve,
> >>
> >>   I've backported openbabel3 from 20.04 to 18.04. You can
> >> download a
> >> tarball with all the deb files in here:
> >>
> >>
> >> http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz
> >>
> >> <
> http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz>
> >>
> >> Kevin
> >>
> >> On 3/15/21 10:10 AM, Hervé Pagès wrote:
> >>  > Hi Thomas, Kevin,
> >>  >
> >>  > We still need to install the system deps on the devel Windows
> >> builders
> >>  > (riesling1 and tokay2). We'll do it this week. Thanks for the
> >> reminder
> >>  > and for making the OpenBabel-3.0.0 Windows Binaries available on
> >> your
> >>  > GitHub repo.
> >>  >
> >>  > Note that OpenBabel 3 is installed on machv2 (devel macOS
> >> builders):
> >>  >
> >>  >   machv2:~ biocbuild$ which obabel
> >>  >   /usr/local/bin/obabel
> >>  >
> >>  >   machv2:~ biocbuild$ obabel -V
> >>  >   Open Babel 3.1.0 -- Oct 21 2020 -- 21:57:42
> >>  >
> >>  >   machv2:~ biocbuild$ pkg-config --cflags openbabel-3
> >>  >   -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3
> >>  >
> >>  >   machv2:~ biocbuild$ pkg-config --libs openbabel-3
> >>  >   -L/usr/local/Cellar/open-babel/3.1.1_1/lib -lopenbabel
> >>  >
> >>  > In release: The reason ChemmineOB does not compile on malbec1 is
> >>  > because it requires OpenBabel 3 but malbec1 only has OpenBabel 2
> >> which
> >>  > is what Ubuntu 18.04 comes with. OpenBabel 3 only became
> available
> >>  > starting with Ubuntu 20.04.
> >>  >
> >>  > To workaround this we could propagate the
> ChemmineOB_1.28.2.tar.gz
> >>  > source tarball produced on nebbiolo1 (Ubuntu 20.04), or, if you
> >> know
> >>  > an easy way to get OpenBabel 3 installed on an Ubuntu 18.04
> >> system,
> >>  > let us know and we will do that. The best thing would be to be
> >> able to
> >>  > use a .deb package for this. The easiest the procedure, the more
> >>  > likely people that are still using Ubuntu 18.04 will be able to
> >>  > install ChemmineOB.
> >>  >
> >>  > Best,
> >>  > H.
> >>  >
> >>  >
> >>  >
> >>  > On 3/12/21 11:10 AM, Thomas Girke wrote:
> >>  >> Dear Hervé and Martin,
> >>  >>
> >>  >> It seems the above problem on the Windows builds has been
> >> resolved
> >>  >> for some
> >>  >> time now. However, any updates on Linux in the release branch
> >> are not
> >>  >> taking effect since 

[Bioc-devel] We are working on a bioinformatics project and we need help from you

[Samman Mahmoud]

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Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

[Hervé Pagès]

Hi Thomas, Kevin,

openbabel3 is now on malbec1 (Ubuntu 18.04). Kevin's 
ubuntu_18.04_openbabel3_debs.tar.gz worked like a charm. Thanks for 
making it so easy.


Note that this addition will affect ChemmineOB build/check results on 
malbec1 on Thursday only:



https://bioconductor.org/checkResults/3.12/bioc-LATEST/ChemmineOB/malbec1-install.html

Cheers,
H.


On 3/16/21 10:24 AM, Hervé Pagès wrote:
@Kevin: Thanks for providing openbabel3 for Ubuntu 18.04. Will take a 
look ASAP.


@Thomas: Yes, the Ubuntu 18.04 builds are only used for the BioC 3.12 
builds (release). BioC 3.13 and further BioC releases are/will be using 
Ubuntu >= 20.04.


Best,
H.


On 3/15/21 1:59 PM, Thomas Girke wrote:

Thanks Hervé for your help with this.

Kevin has provided the *.deb package for installing OpenBabel 3.x on 
Ubuntu 18.04. Just in case, below is how we usually install OpenBabel 
3.x.x across different Ubuntu/Debian systems.


BTW: is it correct to assume that the Ubuntu 18.04 builds will be 
discontinued in the next release in April?


Thanks,

Thomas


## Install ChemmineOB with OpenBabel 3.x from source

## First uninstall libopenbabel-dev (which is version 2.x.x) if 
already installed via
sudo apt-get remove libopenbabel-dev; sudo apt-get purge 
libopenbabel-dev; sudo apt-get --purge autoremove libopenbabel-dev

## Some dependencies to install
sudo apt install cmake libeigen3-dev libboost-all-dev
## Clone OpenBabel 3.x.x from GitHub here: 
https://github.com/openbabel/openbabel 


git clone g...@github.com:openbabel/openbabel.git
mkdir build; cd build
cmake ../openbabel
make
sudo make install
## Install ChemmineOB where you provide environment variables 
including header files and ChemmineOB package iprovided as *.tar.gz 
(adjust paths if not correct)
R CMD INSTALL 
--configure-args='--with-openbabel-include=/usr/local/include/openbabel3/ 
--with-openbabel-lib=/usr/local/lib/openbabel/3.1.1' 
ChemmineOB_1.28.0.tar.gz


On Mon, Mar 15, 2021 at 1:12 PM Kevin Horan > wrote:


    Herve,

  I've backported openbabel3 from 20.04 to 18.04. You can
    download a
    tarball with all the deb files in here:


http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz




    Kevin

    On 3/15/21 10:10 AM, Hervé Pagès wrote:
 > Hi Thomas, Kevin,
 >
 > We still need to install the system deps on the devel Windows
    builders
 > (riesling1 and tokay2). We'll do it this week. Thanks for the
    reminder
 > and for making the OpenBabel-3.0.0 Windows Binaries available on
    your
 > GitHub repo.
 >
 > Note that OpenBabel 3 is installed on machv2 (devel macOS 
builders):

 >
 >   machv2:~ biocbuild$ which obabel
 >   /usr/local/bin/obabel
 >
 >   machv2:~ biocbuild$ obabel -V
 >   Open Babel 3.1.0 -- Oct 21 2020 -- 21:57:42
 >
 >   machv2:~ biocbuild$ pkg-config --cflags openbabel-3
 >   -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3
 >
 >   machv2:~ biocbuild$ pkg-config --libs openbabel-3
 >   -L/usr/local/Cellar/open-babel/3.1.1_1/lib -lopenbabel
 >
 > In release: The reason ChemmineOB does not compile on malbec1 is
 > because it requires OpenBabel 3 but malbec1 only has OpenBabel 2
    which
 > is what Ubuntu 18.04 comes with. OpenBabel 3 only became available
 > starting with Ubuntu 20.04.
 >
 > To workaround this we could propagate the ChemmineOB_1.28.2.tar.gz
 > source tarball produced on nebbiolo1 (Ubuntu 20.04), or, if you 
know
 > an easy way to get OpenBabel 3 installed on an Ubuntu 18.04 
system,

 > let us know and we will do that. The best thing would be to be
    able to
 > use a .deb package for this. The easiest the procedure, the more
 > likely people that are still using Ubuntu 18.04 will be able to
 > install ChemmineOB.
 >
 > Best,
 > H.
 >
 >
 >
 > On 3/12/21 11:10 AM, Thomas Girke wrote:
 >> Dear Hervé and Martin,
 >>
 >> It seems the above problem on the Windows builds has been 
resolved

 >> for some
 >> time now. However, any updates on Linux in the release branch
    are not
 >> taking effect since some/all of the Openbabel dependencies are 
not

 >> available on the corresponding Linux build system (here Ubuntu
    18.04).
 >> However, Ubuntu 20.04 seems to be fine but may not be used to
    create the
 >> source download instance at the moment? As a result, the package
    is only
 >> up-to-date for Windows and OSX (ChemmineOB_1.28.2.) but not Linux
 >> (still at
 >> ChemmineOB_1.28.0.tar.gz):
 >>
    http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html
    .
 >> To fix
 >> this, one suggestion would be whether the