subject:"\[Bioc\-devel\] is it possible to disable i386 builds on bioconductor"

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

2021-03-19 Thread Thomas Girke

Awesome. Thanks for all your help!

Thomas

On Fri, Mar 19, 2021 at 2:42 PM Hervé Pagès 
wrote:

> Hi Thomas, Kevin,
>
> Looks like ChemmineOB 1.28.2 is finally green on malbec1 and is now
> available in BioC 3.12 via BiocManager::install():
>
>https://bioconductor.org/checkResults/3.12/bioc-LATEST/ChemmineOB/
>
> Cheers,
> H.
>
>
> On 3/17/21 10:23 AM, Thomas Girke wrote:
> > 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
> > <
> 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>
> >  >>
> >  >>
> > <
> 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
> >  >>

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

2021-03-19 Thread Hervé Pagès


Hi Thomas, Kevin,

Looks like ChemmineOB 1.28.2 is finally green on malbec1 and is now 
available in BioC 3.12 via BiocManager::install():


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

Cheers,
H.


On 3/17/21 10:23 AM, Thomas Girke wrote:

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 mailto:kho...@cs.ucr.edu>
 >> >> 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.

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

2021-03-17 Thread 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

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

2021-03-17 Thread 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

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

2021-03-16 Thread Hervé Pagès

@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 functional build from the
 >> 20.04
 >> system could be pushed instead of 18.04? Not sure whether this
is less
 >> effort than installing the dependencies on 18.04 that may be
 >> discontinued
 >> soon - just a suggestion/question?
 >>
 >> On the development branch the situation is opposite where the
 >> dependencies are missing on Windows and OSX but Linux is fine:
 >>

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

2021-03-15 Thread Thomas Girke

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 functional build from the
> >> 20.04
> >> system could be pushed instead of 18.04? Not sure whether this is less
> >> effort than installing the dependencies on 18.04 that may be
> >> discontinued
> >> soon - just a suggestion/question?
> >>
> >> On the development branch the situation is opposite where the
> >> dependencies are missing on Windows and OSX but Linux is fine:
> >> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/.
> >>
> >> We realize that the dependencies of the ChemmineOB package creates extra
> >> workload for the Bioc team, and we are extremely grateful for the
> >> support
> >> by the Bioc core team. Please let us know if there is anything on our
> >> end
> >> that could be done to resolve this and/or to minimize your workload
> >> as much
> >> as possible.
> >>
> >> Thanks,
> >>
> >> Thomas
> >>
> >> On Mon, Feb 8, 2021 at 10:02 AM Martin Morgan 
> >> wrote:
> >>
> >>> It's likely failing because your package has C source code that
> >>> accesses
> >>> memory in an invalid way. Likely the bug is present on all
> >>> platforms, but
> >>> only apparent, for the tests you have written, on Windows. The

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

2021-03-15 Thread Kevin Horan


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 functional build from the 
20.04

system could be pushed instead of 18.04? Not sure whether this is less
effort than installing the dependencies on 18.04 that may be 
discontinued

soon - just a suggestion/question?

On the development branch the situation is opposite where the
dependencies are missing on Windows and OSX but Linux is fine:
http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/.

We realize that the dependencies of the ChemmineOB package creates extra
workload for the Bioc team, and we are extremely grateful for the 
support
by the Bioc core team. Please let us know if there is anything on our 
end
that could be done to resolve this and/or to minimize your workload 
as much

as possible.

Thanks,

Thomas

On Mon, Feb 8, 2021 at 10:02 AM Martin Morgan 
wrote:

It's likely failing because your package has C source code that 
accesses
memory in an invalid way. Likely the bug is present on all 
platforms, but
only apparent, for the tests you have written, on Windows. The right 
thing

to do is to fix the bug, rather than avoid by not running on the
troublesome platform.

Under Linux you'd likely have success with valgrind or UBSAN; if you 
were
reasonably confident that the package occurred in unit tests, and 
you have

a script to run the unit tests run_tests.R then something like

   R -d valgrind -f run_tests.R

may be productive. valgrind is slow so it pays to narrow the problem 
down

as much as possible.

Maartin

On 2/8/21, 12:43 PM, "Bioc-devel on behalf of Kevin Horan" <
bioc-devel-boun...@r-project.org on behalf of kho...@cs.ucr.edu> wrote:


  I have a package which randomly segfaults when running my 
unit
 tests only on windows i386, but never on x64, or any other OS. 
I can't
 imagine there are many out there still running i386 systems are 
there?
 Is it possible to just disable the i386 build on bioconductor 
so that

 the tests are not run on that architecture?

  I have of course done my best to debug the issue, but all 
I get

is
 an error in some nt dll file, with no useful message or 
location. I'm

I
 Linux guy, I don't know how to do the in-depth debugging that 
would be

 required to track this bug down on windows. I tried disabling each
test
 one by one to see which one caused the crash, but as is typical 
with
 segfaults, changing the setup can mask the bug even when the 
bad code

is
 still be executed. Each test runs fine in isolation.

 Thanks

 Kevin

 ___
 Bioc-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2021-03-15 Thread Hervé Pagès


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 functional build from the 20.04
system could be pushed instead of 18.04? Not sure whether this is less
effort than installing the dependencies on 18.04 that may be discontinued
soon - just a suggestion/question?

On the development branch the situation is opposite where the
dependencies are missing on Windows and OSX but Linux is fine:
http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/.

We realize that the dependencies of the ChemmineOB package creates extra
workload for the Bioc team, and we are extremely grateful for the support
by the Bioc core team. Please let us know if there is anything on our end
that could be done to resolve this and/or to minimize your workload as much
as possible.

Thanks,

Thomas

On Mon, Feb 8, 2021 at 10:02 AM Martin Morgan 
wrote:


It's likely failing because your package has C source code that accesses
memory in an invalid way. Likely the bug is present on all platforms, but
only apparent, for the tests you have written, on Windows. The right thing
to do is to fix the bug, rather than avoid by not running on the
troublesome platform.

Under Linux you'd likely have success with valgrind or UBSAN; if you were
reasonably confident that the package occurred in unit tests, and you have
a script to run the unit tests run_tests.R then something like

   R -d valgrind -f run_tests.R

may be productive. valgrind is slow so it pays to narrow the problem down
as much as possible.

Maartin

On 2/8/21, 12:43 PM, "Bioc-devel on behalf of Kevin Horan" <
bioc-devel-boun...@r-project.org on behalf of kho...@cs.ucr.edu> wrote:


  I have a package which randomly segfaults when running my unit
 tests only on windows i386, but never on x64, or any other OS. I can't
 imagine there are many out there still running i386 systems are there?
 Is it possible to just disable the i386 build on bioconductor so that
 the tests are not run on that architecture?

  I have of course done my best to debug the issue, but all I get
is
 an error in some nt dll file, with no useful message or location. I'm
I
 Linux guy, I don't know how to do the in-depth debugging that would be
 required to track this bug down on windows. I tried disabling each
test
 one by one to see which one caused the crash, but as is typical with
 segfaults, changing the setup can mask the bug even when the bad code
is
 still be executed. Each test runs fine in isolation.

 Thanks

 Kevin

 ___
 Bioc-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel






--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

___
Bioc-devel@r-project.org mailing

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

2021-03-12 Thread Thomas Girke

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 functional build from the 20.04
system could be pushed instead of 18.04? Not sure whether this is less
effort than installing the dependencies on 18.04 that may be discontinued
soon - just a suggestion/question?

On the development branch the situation is opposite where the
dependencies are missing on Windows and OSX but Linux is fine:
http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/.

We realize that the dependencies of the ChemmineOB package creates extra
workload for the Bioc team, and we are extremely grateful for the support
by the Bioc core team. Please let us know if there is anything on our end
that could be done to resolve this and/or to minimize your workload as much
as possible.

Thanks,

Thomas

On Mon, Feb 8, 2021 at 10:02 AM Martin Morgan 
wrote:

> It's likely failing because your package has C source code that accesses
> memory in an invalid way. Likely the bug is present on all platforms, but
> only apparent, for the tests you have written, on Windows. The right thing
> to do is to fix the bug, rather than avoid by not running on the
> troublesome platform.
>
> Under Linux you'd likely have success with valgrind or UBSAN; if you were
> reasonably confident that the package occurred in unit tests, and you have
> a script to run the unit tests run_tests.R then something like
>
>   R -d valgrind -f run_tests.R
>
> may be productive. valgrind is slow so it pays to narrow the problem down
> as much as possible.
>
> Maartin
>
> On 2/8/21, 12:43 PM, "Bioc-devel on behalf of Kevin Horan" <
> bioc-devel-boun...@r-project.org on behalf of kho...@cs.ucr.edu> wrote:
>
>
>  I have a package which randomly segfaults when running my unit
> tests only on windows i386, but never on x64, or any other OS. I can't
> imagine there are many out there still running i386 systems are there?
> Is it possible to just disable the i386 build on bioconductor so that
> the tests are not run on that architecture?
>
>  I have of course done my best to debug the issue, but all I get
> is
> an error in some nt dll file, with no useful message or location. I'm
> I
> Linux guy, I don't know how to do the in-depth debugging that would be
> required to track this bug down on windows. I tried disabling each
> test
> one by one to see which one caused the crash, but as is typical with
> segfaults, changing the setup can mask the bug even when the bad code
> is
> still be executed. Each test runs fine in isolation.
>
> Thanks
>
> Kevin
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Thomas Girke, Ph.D.
Professor of Bioinformatics
1207F Genomics Building
University of California
Riverside, CA 92521

E-mail: thomas.gi...@ucr.edu
URL: https://girke.bioinformatics.ucr.edu
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437

[[alternative HTML version deleted]]

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

2021-02-08 Thread Martin Morgan

It's likely failing because your package has C source code that accesses memory 
in an invalid way. Likely the bug is present on all platforms, but only 
apparent, for the tests you have written, on Windows. The right thing to do is 
to fix the bug, rather than avoid by not running on the troublesome platform.

Under Linux you'd likely have success with valgrind or UBSAN; if you were 
reasonably confident that the package occurred in unit tests, and you have a 
script to run the unit tests run_tests.R then something like

  R -d valgrind -f run_tests.R

may be productive. valgrind is slow so it pays to narrow the problem down as 
much as possible.

Maartin

On 2/8/21, 12:43 PM, "Bioc-devel on behalf of Kevin Horan" 
 wrote:


 I have a package which randomly segfaults when running my unit 
tests only on windows i386, but never on x64, or any other OS. I can't 
imagine there are many out there still running i386 systems are there? 
Is it possible to just disable the i386 build on bioconductor so that 
the tests are not run on that architecture?

 I have of course done my best to debug the issue, but all I get is 
an error in some nt dll file, with no useful message or location. I'm I 
Linux guy, I don't know how to do the in-depth debugging that would be 
required to track this bug down on windows. I tried disabling each test 
one by one to see which one caused the crash, but as is typical with 
segfaults, changing the setup can mask the bug even when the bad code is 
still be executed. Each test runs fine in isolation.

Thanks

Kevin

___
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https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2021-02-08 Thread Kevin Horan




    I have a package which randomly segfaults when running my unit 
tests only on windows i386, but never on x64, or any other OS. I can't 
imagine there are many out there still running i386 systems are there? 
Is it possible to just disable the i386 build on bioconductor so that 
the tests are not run on that architecture?


    I have of course done my best to debug the issue, but all I get is 
an error in some nt dll file, with no useful message or location. I'm I 
Linux guy, I don't know how to do the in-depth debugging that would be 
required to track this bug down on windows. I tried disabling each test 
one by one to see which one caused the crash, but as is typical with 
segfaults, changing the setup can mask the bug even when the bad code is 
still be executed. Each test runs fine in isolation.


Thanks

Kevin

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

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

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

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

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

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

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

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

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

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

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

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