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

Dear Herv? 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 <mtmorgan.bioc at gmail.com>
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-bounces at r-project.org on behalf of khoran at 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

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 Herv? 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 <mtmorgan.bioc at gmail.com>
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-bounces at r-project.org on behalf of khoran at 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 at r-project.org mailing list
???? https://stat.ethz.ch/mailman/listinfo/bioc-devel

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, Herv? Pag?s 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 Herv? 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 <mtmorgan.bioc at gmail.com>
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-bounces at r-project.org on behalf of khoran at 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

Thanks Herv? 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 
<https://github.com/openbabel/openbabel>
git clone git at 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 <khoran at cs.ucr.edu 
<mailto:khoran at 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
    <http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz>

    Kevin

    On 3/15/21 10:10 AM, Herv? Pag?s 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 Herv? 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
    <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/
    <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

    <mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>>

     >> 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-bounces at r-project.org

    <mailto:bioc-devel-bounces at r-project.org> on behalf of
    khoran at cs.ucr.edu <mailto:khoran at 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 at r-project.org <mailto:Bioc-devel at r-project.org>

    mailing list

     >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>

     >>> _______________________________________________
     >>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>

    mailing list

     >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <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.girke at ucr.edu <mailto:thomas.girke at ucr.edu>
URL: https://girke.bioinformatics.ucr.edu 
<https://girke.bioinformatics.ucr.edu>
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437

@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 Herv? 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 
<https://github.com/openbabel/openbabel>
git clone git at 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 <khoran at cs.ucr.edu 
<mailto:khoran at 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
    
<http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz>

??? Kevin

??? On 3/15/21 10:10 AM, Herv? Pag?s 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 Herv? 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
??? <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/
??? <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
??? <mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>>
???? >> 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-bounces at r-project.org
??? <mailto:bioc-devel-bounces at r-project.org> on behalf of
??? khoran at cs.ucr.edu <mailto:khoran at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
??? mailing list
???? >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
??? <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
???? >>> _______________________________________________
???? >>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
??? mailing list
???? >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
??? <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.girke at ucr.edu <mailto:thomas.girke at ucr.edu>
URL: https://girke.bioinformatics.ucr.edu 
<https://girke.bioinformatics.ucr.edu>
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437

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, Herv? Pag?s 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 Herv? 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
<https://github.com/openbabel/openbabel>
git clone git at 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 <khoran at cs.ucr.edu
<mailto:khoran at 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

<

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

    Kevin

    On 3/15/21 10:10 AM, Herv? Pag?s 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 Herv? 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
    <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/
    <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

    <mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>>

     >> 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-bounces at r-project.org

    <mailto:bioc-devel-bounces at r-project.org> on behalf of
    khoran at cs.ucr.edu <mailto:khoran at 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 at r-project.org <mailto:Bioc-devel at r-project.org>

    mailing list

     >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>

     >>> _______________________________________________
     >>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>

    mailing list

     >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <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.girke at ucr.edu <mailto:thomas.girke at ucr.edu>
URL: https://girke.bioinformatics.ucr.edu
<https://girke.bioinformatics.ucr.edu>
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437

--
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com

Awesome, thanks!

On Tue, Mar 16, 2021 at 11:40 PM Herv? Pag?s <hpages.on.github at gmail.com 
<mailto:hpages.on.github at gmail.com>> 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, Herv? Pag?s 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 Herv? 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

    <https://github.com/openbabel/openbabel>

     >> <https://github.com/openbabel/openbabel

    <https://github.com/openbabel/openbabel>>

     >> git clone git at 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 <khoran at cs.ucr.edu

    <mailto:khoran at cs.ucr.edu>

     >> <mailto:khoran at cs.ucr.edu <mailto:khoran at 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
    <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, Herv? Pag?s 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 Herv? 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
    <http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html>

     >>    

    <http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html
    <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/
    <http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/>

     >>    

    <http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/
    <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
     >> ??? <mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>

    <mailto:mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>>>

     >> ???? >> 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-bounces at r-project.org

    <mailto:bioc-devel-bounces at r-project.org>

     >> ??? <mailto:bioc-devel-bounces at r-project.org

    <mailto:bioc-devel-bounces at r-project.org>> on behalf of

     >> khoran at cs.ucr.edu <mailto:khoran at cs.ucr.edu>

    <mailto:khoran at cs.ucr.edu <mailto:khoran at 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 at r-project.org

    <mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org
    <mailto:Bioc-devel at r-project.org>>

     >> ??? mailing list
     >> ???? >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>

     >> ??? <https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>

     >> ???? >>> _______________________________________________
     >> ???? >>> Bioc-devel at r-project.org

    <mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org
    <mailto:Bioc-devel at r-project.org>>

     >> ??? mailing list
     >> ???? >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>

     >> ??? <https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <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.girke at ucr.edu <mailto:thomas.girke at ucr.edu>

    <mailto:thomas.girke at ucr.edu <mailto:thomas.girke at ucr.edu>>

     >> URL: https://girke.bioinformatics.ucr.edu

    <https://girke.bioinformatics.ucr.edu>

     >> <https://girke.bioinformatics.ucr.edu

    <https://girke.bioinformatics.ucr.edu>>

     >> Phone/Cell/Text: 951-732-7072
     >> Fax: 951-827-4437

     >

    -- 
    Herv? Pag?s

    Bioconductor Core Team
    hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com>



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

E-mail: thomas.girke at ucr.edu <mailto:thomas.girke at ucr.edu>
URL: https://girke.bioinformatics.ucr.edu 
<https://girke.bioinformatics.ucr.edu>
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437

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 Herv? Pag?s <hpages.on.github at gmail.com
<mailto:hpages.on.github at gmail.com>> 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, Herv? Pag?s 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 Herv? 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

    <https://github.com/openbabel/openbabel>

     >> <https://github.com/openbabel/openbabel

    <https://github.com/openbabel/openbabel>>

     >> git clone git at 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 <khoran at cs.ucr.edu

    <mailto:khoran at cs.ucr.edu>

     >> <mailto:khoran at cs.ucr.edu <mailto:khoran at 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

    <

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, Herv? Pag?s 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 Herv? 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
    <http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html>

     >>

    <http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html
    <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/
    <http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/>

     >>

    <http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/
    <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

     >>     <mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>

    <mailto:mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>>>

     >>      >> 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-bounces at r-project.org

    <mailto:bioc-devel-bounces at r-project.org>

     >>     <mailto:bioc-devel-bounces at r-project.org

    <mailto:bioc-devel-bounces at r-project.org>> on behalf of

     >> khoran at cs.ucr.edu <mailto:khoran at cs.ucr.edu>

    <mailto:khoran at cs.ucr.edu <mailto:khoran at 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 at r-project.org

    <mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org
    <mailto:Bioc-devel at r-project.org>>

     >>     mailing list

     >>      >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>

     >>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>

     >>      >>> _______________________________________________
     >>      >>> Bioc-devel at r-project.org

    <mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org
    <mailto:Bioc-devel at r-project.org>>

     >>     mailing list

     >>      >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>

     >>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel

    <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.girke at ucr.edu <mailto:thomas.girke at ucr.edu>

    <mailto:thomas.girke at ucr.edu <mailto:thomas.girke at ucr.edu>>

     >> URL: https://girke.bioinformatics.ucr.edu

    <https://girke.bioinformatics.ucr.edu>

     >> <https://girke.bioinformatics.ucr.edu

    <https://girke.bioinformatics.ucr.edu>>

     >> Phone/Cell/Text: 951-732-7072
     >> Fax: 951-827-4437

     >

    --
    Herv? Pag?s

    Bioconductor Core Team
    hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com>



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

E-mail: thomas.girke at ucr.edu <mailto:thomas.girke at ucr.edu>
URL: https://girke.bioinformatics.ucr.edu
<https://girke.bioinformatics.ucr.edu>
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437

--
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com