[Bioc-devel] missing packages on nebbiolo1

[Kevin Horan]

The packages eiR and ChemmineOB are failing to build because nebbiolo1 
is missing the packages RUnit and RSQLite. Could those be installed 
please? Thank you.


https://master.bioconductor.org/checkResults/3.17/bioc-LATEST/eiR/nebbiolo1-checksrc.html

https://master.bioconductor.org/checkResults/3.17/bioc-LATEST/ChemmineOB/nebbiolo1-checksrc.html

Kevin

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

[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

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

[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] ChemmineOB build failing on windows

[Kevin Horan]

Hervé,

    It could be. The test I did today was on a clean windows machine, 
so I did build open babel from scratch with Rtools40. I don't have an 
openbabel built with the old version to check. The INSTALL file of 
ChemmineOB provides detail instructions for building OpenBabel on windows.


Kevin

On 4/23/20 12:52 PM, Hervé Pagès wrote:

On 4/23/20 12:45, Hervé Pagès wrote:

On 4/23/20 10:45, Kevin Horan wrote:

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 
3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to 
build the package on my own windows machine (Windows Server 2012 R2 
Standard) without any error. I used R devel. The content of this 
package has not been changed since October 2018.


Right but the toolchain used for R 4.0.0 on Windows now is Rtool40 
which is a huge upgrade from the previous one. Could this be related 
to the compilation failure?


It also occurs to me that we might need to recompile Open Babel with 
the new toolchain on tokay2. Could that be the problem?


H.



Best,
H.



Can someone please look into it? Thanks. The build link is 
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineOB_tokay2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM=hoMGH754DpRKnA8RGcuSStVub2IwW2BGrG6lvBK4io4= 



Kevin

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[Bioc-devel] ChemmineOB build failing on windows

[Kevin Horan]

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 3 
other packages to fail (ChemmineR, eiR, and fmcsR). I was able to build 
the package on my own windows machine (Windows Server 2012 R2 Standard) 
without any error. I used R devel. The content of this package has not 
been changed since October 2018.


Can someone please look into it? Thanks. The build link is 
https://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/tokay2-buildsrc.html



Kevin

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[Bioc-devel] current openbabel version on tokay2

[Kevin Horan]

I have a build error on my ChemmineOB package on windows, Tokay2. So 
that I can try to reproduce the error locally, could you let me know 
what version of OpenBabel is on that machine? My assumption would be 
that it is 2.4.1. It's not an R package, so it's not listed on your 
website. Thanks.


Kevin Horan

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[Bioc-devel] rsvg missing on merida2

[Kevin Horan]

My package, ChemmineR, is failing to build because of a missing 
package, rsvg. This package was there during the last release cycle, and 
is still present on the release build machines. I'm just wondering if 
this package is going to return or not? It's been about a week since the 
build broke. Thanks.


http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html

ERROR: dependency ‘rsvg’ is not available for package ‘ChemmineR’
* removing 
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ChemmineR’



Kevin

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Re: [Bioc-devel] rsvg on mac

[Kevin Horan]

Valerie,

 ��� Sorry, I think my memory of what the actual problem was was wrong. 
I have spoken to the rsvg author and he has now fixed the build of rsvg 
in CRAN for OS X. So will that then just get automatically put on your 
machines, or else, would it now be possible to manually put it on? Sorry 
for all the confusion, and thanks for you help.

 ��� ChemmineR is green now because I removed the functions requiring 
rsvg to get it through the release. They were new functions anyway.

Kevin


On 05/09/2018 03:25 PM, Obenchain, Valerie wrote:
> Kevin,
>
> I feel like we're not on the same page. We've had this discussion and 
> both Herve and I tried to explain the situation:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-February/012812.html
>
> We do not build CRAN packages from source on the Windows and Mac build 
> machines. If a CRAN binary is not available for one of your 
> dependencies, e.g., rsvg, the best thing for you to do is contact the 
> maintainer or post on the r-sig-mac mailing list:
>
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> However, ChemmineR is green on both release and devel build reports. 
> I'm not sure why you are asking us (again) to install the rsvg system 
> dependency on the Mac builders. Did I misunderstand what you wanted?
>
> Valerie
>
>
> On 05/09/2018 07:41 AM, Kevin Horan wrote:
>>
>> ��� Now that this past bioc release is done, and R 3.5 is stable, 
>> would it be possible to install the "rsvg" package on your build 
>> machines? Thanks.
>>
>> Kevin
>>
>>
>> On 02/19/2018 02:01 PM, Alexey Sergushichev wrote:
>>> Valerie, thanks. Will try to ask there.
>>>
>>> However, after looking through the mailing list it looks like 
>>> R-devel builds for OS X aren't trivial and aren't part of CRAN...
>>>
>>> --
>>> Alexey
>>>
>>> On Mon, Feb 19, 2018 at 9:05 PM, Obenchain, Valerie 
>>> <valerie.obench...@roswellpark.org 
>>> <mailto:valerie.obench...@roswellpark.org>> wrote:
>>>
>>> Hi,
>>>
>>> There has been some discussion of the devel Mac binaries on the
>>> R-SIG-Mac mailing list. That list would be the best place to ask
>>> this question.
>>>
>>> https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html
>>> <https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html>
>>>
>>> Valerie
>>>
>>>
>>>
>>> On 02/19/2018 08:32 AM, Alexey Sergushichev wrote:
>>>> Valerie,
>>>>
>>>> Are there any estimates on how often CRAN OS X builds happen?
>>>> There are still no builds for rsvg and other packages...
>>>>
>>>> Thanks,
>>>> Alexey
>>>>
>>>> On Wed, Feb 7, 2018 at 8:09 PM, Obenchain, Valerie
>>>> <valerie.obench...@roswellpark.org
>>>> <mailto:valerie.obench...@roswellpark.org>> wrote:
>>>>
>>>> Hi Kevin,
>>>>
>>>> CRAN binaries for El Capitan in devel aren't available. You
>>>> can see this on the rsvg landing page:
>>>>
>>>> https://cran.r-project.org/web/packages/rsvg/index.html
>>>> <https://cran.r-project.org/web/packages/rsvg/index.html>
>>>>
>>>> Nothing we can do until CRAN makes them available.
>>>>
>>>> Valerie
>>>>
>>>>
>>>> On 02/07/2018 08:29 AM, Kevin Horan wrote:
>>>>
>>>>
>>>> The ChemmineR build is failing on the mac due to a new
>>>> dependency not
>>>> being available, the package "rsvg". Would it be possible
>>>> to install
>>>> that on the mac build machine? Thanks.
>>>>
>>>> 
>>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html
>>>> 
>>>> <http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html>
>>>>
>>>>
>>>> Kevin
>>>>
>>>> ___
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Re: [Bioc-devel] rsvg on mac

[Kevin Horan]

     Now that this past bioc release is done, and R 3.5 is stable, would 
it be possible to install the "rsvg" package on your build machines? Thanks.

Kevin


On 02/19/2018 02:01 PM, Alexey Sergushichev wrote:
> Valerie, thanks. Will try to ask there.
>
> However, after looking through the mailing list it looks like R-devel 
> builds for OS X aren't trivial and aren't part of CRAN...
>
> --
> Alexey
>
> On Mon, Feb 19, 2018 at 9:05 PM, Obenchain, Valerie 
> <valerie.obench...@roswellpark.org 
> <mailto:valerie.obench...@roswellpark.org>> wrote:
>
> Hi,
>
> There has been some discussion of the devel Mac binaries on the
> R-SIG-Mac mailing list. That list would be the best place to ask
> this question.
>
> https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html
> <https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html>
>
> Valerie
>
>
>
> On 02/19/2018 08:32 AM, Alexey Sergushichev wrote:
>> Valerie,
>>
>> Are there any estimates on how often CRAN OS X builds happen?
>> There are still no builds for rsvg and other packages...
>>
>> Thanks,
>> Alexey
>>
>> On Wed, Feb 7, 2018 at 8:09 PM, Obenchain, Valerie
>> <valerie.obench...@roswellpark.org
>> <mailto:valerie.obench...@roswellpark.org>> wrote:
>>
>> Hi Kevin,
>>
>> CRAN binaries for El Capitan in devel aren't available. You
>> can see this on the rsvg landing page:
>>
>> https://cran.r-project.org/web/packages/rsvg/index.html
>> <https://cran.r-project.org/web/packages/rsvg/index.html>
>>
>> Nothing we can do until CRAN makes them available.
>>
>> Valerie
>>
>>
>> On 02/07/2018 08:29 AM, Kevin Horan wrote:
>>
>>
>> The ChemmineR build is failing on the mac due to a new
>> dependency not
>> being available, the package "rsvg". Would it be possible to
>> install
>> that on the mac build machine? Thanks.
>>
>> 
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html
>> 
>> <http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html>
>>
>>
>> Kevin
>>
>> ___
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Re: [Bioc-devel] rsvg on mac

[Kevin Horan]

Ok, I understand. Is it safe to assume that the rsvg package would be 
available by the time the next bioconductor release occurs? In that case 
I can just plan to re-enable that function at release time. Otherwise I 
will have to find another workaround for it. Thanks.



Kevin


On 02/13/2018 05:24 PM, Hervé Pagès wrote:

Hi Kevin,

As Val said, some CRAN packages with native code won't compile
on our Windows or Mac builders because of missing components,
and rsvg is one of them. Please keep in mind that we already
install many external components required for the compilation
of Bioconductor packages. The process of doing so on a fresh
Mac El Capitan system is documented here:


https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-MacOSX-El-Capitan-HOWTO.TXT 



Installing these components is time consuming and there is always
the risk to introduce some conflicts/instabilities when installing
new components. Given that our resources are limited, it wouldn't
make much sense that we do this for those CRAN packages for which
the binaries are only temporarily unavailable.

Cheers,
H.


On 02/13/2018 12:56 PM, Kevin Horan wrote:

Valerie,

  Ok, I understand the difference now. Would it be possible to
install the system requirement for rsvg ( just on devel)?

  I'm trying to generate plots in either PNG or SVG with OpenBabel.
For PNG, OpenBabel requires it's own Cario library be installed on the
system (doesn't seem to work with what is built into R, as it needs to
be linked with OpenBabel). I've not been successful getting the Cairo
lib installed on windows, but using SVG with OpenBabel, and then reading
that back into R with rsvg, works fine. So it seems I'll need a extra
system library either way ( either Cairo, or librsvg2).

Thanks.

Kevin


On 02/13/2018 06:43 AM, Obenchain, Valerie wrote:

Hi,

By default, the build system installs CRAN dependencies on the Mac and
Windows builders with 'type=both':

   install.packages("mypackage", type="both")

This means it first tries to install the binary and if that fails, it
tries to install from source. Packages without native code or
SystemRequirements usually install fine from source. This is the case
for DiagrammeR which can be installed on the build machines. rsvg is
in the Suggests field of DiagrammeR so rsvg is not needed to install
or load the package.

The rsvg package is different in that it has 'librsvg2' as a
SystemRequirement which is not installed on the Mac (or Windows) build
machine:

https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w= 



We do install all SystemRequirements for Bioconductor packages on the
Mac and Windows builders but not for CRAN packages. Installing all
third party requirements of CRAN dependencies would add significantly
to the build system maintenance and really only serves a purpose in
this window of time where binaries are not available for devel.

cc'ing Herve in case he has more to add.


Valerie




On 02/12/2018 12:25 PM, Kevin Horan wrote:

Valerie,
 I'm not sure I understand. I looked at another package that is
currently installed on the mac devel machine, DiagrammeR
(https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_package-3DDiagrammeR=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=7UDK9omF9qsdLzWH6wEh_fyNE5BuQbNbJzc0v925ElE=), 
and it has the same

set of links on the CRAN site as rsvg does. In particular, it does
not show a  r-devel version for El Capitan.
 Also, rsvg is not installed on the release mac build machine
either, which it should have a version for.

Kevin

On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:

Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see
this on the rsvg landing page:

https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w= 



Nothing we can do until CRAN makes them available.

Valerie


On 02/07/2018 08:29 AM, Kevin Horan wrote:
The ChemmineR build is failing on the mac due to a new dependency 
not

being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineR_merida2-2Dinstall.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=B43U-waIixUyD4yJS4OySSIX5jVaAXp98jUM348m8oU= 




Kevin

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Re: [Bioc-devel] rsvg on mac

[Kevin Horan]

Valerie,

 Ok, I understand the difference now. Would it be possible to 
install the system requirement for rsvg ( just on devel)?

 I'm trying to generate plots in either PNG or SVG with OpenBabel. 
For PNG, OpenBabel requires it's own Cario library be installed on the 
system (doesn't seem to work with what is built into R, as it needs to 
be linked with OpenBabel). I've not been successful getting the Cairo 
lib installed on windows, but using SVG with OpenBabel, and then reading 
that back into R with rsvg, works fine. So it seems I'll need a extra 
system library either way ( either Cairo, or librsvg2).

Thanks.

Kevin


On 02/13/2018 06:43 AM, Obenchain, Valerie wrote:
> Hi,
>
> By default, the build system installs CRAN dependencies on the Mac and 
> Windows builders with 'type=both':
>
>   install.packages("mypackage", type="both")
>
> This means it first tries to install the binary and if that fails, it 
> tries to install from source. Packages without native code or 
> SystemRequirements usually install fine from source. This is the case 
> for DiagrammeR which can be installed on the build machines. rsvg is 
> in the Suggests field of DiagrammeR so rsvg is not needed to install 
> or load the package.
>
> The rsvg package is different in that it has 'librsvg2' as a 
> SystemRequirement which is not installed on the Mac (or Windows) build 
> machine:
>
> https://cran.r-project.org/web/packages/rsvg/index.html
>
> We do install all SystemRequirements for Bioconductor packages on the 
> Mac and Windows builders but not for CRAN packages. Installing all 
> third party requirements of CRAN dependencies would add significantly 
> to the build system maintenance and really only serves a purpose in 
> this window of time where binaries are not available for devel.
>
> cc'ing Herve in case he has more to add.
>
>
> Valerie
>
>
>
>
> On 02/12/2018 12:25 PM, Kevin Horan wrote:
>> Valerie,
>> I'm not sure I understand. I looked at another package that is 
>> currently installed on the mac devel machine, DiagrammeR 
>> (https://cran.r-project.org/package=DiagrammeR), and it has the same 
>> set of links on the CRAN site as rsvg does. In particular, it does 
>> not show a  r-devel version for El Capitan.
>> Also, rsvg is not installed on the release mac build machine 
>> either, which it should have a version for.
>>
>> Kevin
>>
>> On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:
>>> Hi Kevin,
>>>
>>> CRAN binaries for El Capitan in devel aren't available. You can see 
>>> this on the rsvg landing page:
>>>
>>> https://cran.r-project.org/web/packages/rsvg/index.html
>>>
>>> Nothing we can do until CRAN makes them available.
>>>
>>> Valerie
>>>
>>>
>>> On 02/07/2018 08:29 AM, Kevin Horan wrote:
>>>> The ChemmineR build is failing on the mac due to a new dependency not
>>>> being available, the package "rsvg". Would it be possible to install
>>>> that on the mac build machine? Thanks.
>>>>
>>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html
>>>>
>>>>
>>>> Kevin
>>>>
>>>> ___
>>>> Bioc-devel@r-project.org  mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>> This email message may contain legally privileged and/or 
>>> confidential information. If you are not the intended recipient(s), 
>>> or the employee or agent responsible for the delivery of this 
>>> message to the intended recipient(s), you are hereby notified that 
>>> any disclosure, copying, distribution, or use of this email message 
>>> is prohibited. If you have received this message in error, please 
>>> notify the sender immediately by e-mail and delete this email 
>>> message from your computer. Thank you. 
>>
>
>
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee 
> or agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately 
> by e-mail and delete this email message from your computer. Thank you. 


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Re: [Bioc-devel] release build of ChemmineR failing

[Kevin Horan]

Andrzej,
 Sorry, I didn't realize that line was coming from my own Makefile. 
The Makefile was there for historic reasons, but I think can be removed 
now, so that will probably fix the problem.

Kevin

On 02/08/2018 02:39 AM, Andrzej Oleś wrote:
> Dear Kevin,
>
> thank you for reporting the problem. It is not clear to me why do you 
> need a Makefile to build your vignette in first place, could you maybe 
> explain the motivation behind it?
>
> Cheers,
> Andrzej
>
>
> On Wed, Feb 7, 2018 at 5:37 PM, Kevin Horan 
> <kho...@globalrecordings.net <mailto:kho...@globalrecordings.net>> wrote:
>
> The release version of ChemmineR is failing on windows. It seems
> to be a
> build script issue though, possibly something on your side. The
> package
> was building fine a few weeks ago and I have not modified it. Can you
> please have a look? Thanks.
>
> "C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e
> "library(rmarkdown); library(BiocStyle);
> rmarkdown::render('ChemmineR.Rmd')"
> 'C:\Users\BIOCBU˜1\BBS-3˜1.6-B\R\bin\x64\Rscript.exe" -e "library'
> is not recognized as an internal or external command,operable
> program or batch file.
>
> 
> http://bioconductor.org/checkResults/release/bioc-LATEST/ChemmineR/tokay1-buildsrc.html
> 
> <http://bioconductor.org/checkResults/release/bioc-LATEST/ChemmineR/tokay1-buildsrc.html>
>
>
> Kevin
>
> ___
> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing
> list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>
>


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Re: [Bioc-devel] rsvg on mac

[Kevin Horan]

Valerie,
 I'm not sure I understand. I looked at another package that is 
currently installed on the mac devel machine, DiagrammeR 
(https://cran.r-project.org/package=DiagrammeR), and it has the same set 
of links on the CRAN site as rsvg does. In particular, it does not show 
a  r-devel version for El Capitan.
 Also, rsvg is not installed on the release mac build machine 
either, which it should have a version for.

Kevin

On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:
> Hi Kevin,
>
> CRAN binaries for El Capitan in devel aren't available. You can see 
> this on the rsvg landing page:
>
> https://cran.r-project.org/web/packages/rsvg/index.html
>
> Nothing we can do until CRAN makes them available.
>
> Valerie
>
>
> On 02/07/2018 08:29 AM, Kevin Horan wrote:
>> The ChemmineR build is failing on the mac due to a new dependency not
>> being available, the package "rsvg". Would it be possible to install
>> that on the mac build machine? Thanks.
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html
>>
>>
>> Kevin
>>
>> ___
>> Bioc-devel@r-project.org  mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee 
> or agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately 
> by e-mail and delete this email message from your computer. Thank you. 


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[Bioc-devel] release build of ChemmineR failing

[Kevin Horan]

The release version of ChemmineR is failing on windows. It seems to be a
build script issue though, possibly something on your side. The package
was building fine a few weeks ago and I have not modified it. Can you
please have a look? Thanks.

"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e "library(rmarkdown); 
library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
'C:\Users\BIOCBU˜1\BBS-3˜1.6-B\R\bin\x64\Rscript.exe" -e "library' is not 
recognized as an internal or external command,operable program or batch file.

http://bioconductor.org/checkResults/release/bioc-LATEST/ChemmineR/tokay1-buildsrc.html


Kevin

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[Bioc-devel] release build of ChemmineR failing

[Kevin Horan]

The release version of ChemmineR is failing on windows. It seems to be a
build script issue though, possibly something on your side. The package
was building fine a few weeks ago and I have not modified it. Can you
please have a look? Thanks.

"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e "library(rmarkdown); 
library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
'C:\Users\BIOCBU˜1\BBS-3˜1.6-B\R\bin\x64\Rscript.exe" -e "library' is 
not recognized as an internal or external command,operable program or 
batch file.


http://bioconductor.org/checkResults/release/bioc-LATEST/ChemmineR/tokay1-buildsrc.html


Kevin

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[Bioc-devel] rsvg on mac

[Kevin Horan]

The ChemmineR build is failing on the mac due to a new dependency not 
being available, the package "rsvg". Would it be possible to install 
that on the mac build machine? Thanks.


http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html


Kevin

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[Rd] release build of ChemmineR failing

[Kevin Horan]

The release version of ChemmineR is failing on windows. It seems to be a 
build script issue though, possibly something on your side. The package 
was building fine a few weeks ago and I have not modified it. Can you 
please have a look? Thanks.

"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e "library(rmarkdown); 
library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
'C:\Users\BIOCBU˜1\BBS-3˜1.6-B\R\bin\x64\Rscript.exe" -e "library' is not 
recognized as an internal or external command,operable program or batch file.

http://bioconductor.org/checkResults/release/bioc-LATEST/ChemmineR/tokay1-buildsrc.html
 


Kevin


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[Rd] rsvg on mac

[Kevin Horan]

The ChemmineR build is failing on the mac due to a new dependency not 
being available, the package "rsvg". Would it be possible to install 
that on the mac build machine? Thanks.


http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html


Kevin

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Re: [Bioc-devel] git help

[Kevin Horan]

Nitesh,

  I have re-cloned it, everything looks good. Thanks for your help.

Can you please make sure that the duplicate commit check has been 
re-enabled for this repo? It was previously disabled.



Kevin


On 01/09/2018 10:03 AM, Turaga, Nitesh wrote:

Hi Kevin,

Your repository should now be fixed.  Please re-clone your repository.

Best,

Nitesh

On Jan 8, 2018, at 8:39 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

Sorry, just saw your email now. You can go ahead and make those changes. 
Thanks for all your help.

Kevin


On 01/07/2018 11:22 AM, Turaga, Nitesh wrote:

Hi Kevin,

One last message, give me a green light to fix your repository once you have 
had a chance to see my emails.

Best,

Nitesh


On Jan 7, 2018, at 2:17 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
wrote:

Now your version numbers don’t match. You skip versions without those commits

Your history is supposed to look like this,

commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran <kho...@cs.ucr.edu>
Date:   Sun Jan 7 09:44:16 2018 -0800

History was rolled back 6 months to remove dup commits.
All changes since then are being re-applied in this one commit.

commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <kho...@cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
 bc3139a8-67e5-0310-9ffc-ced21a209358

##
Same for the RELEASE branch.
##

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran <kho...@cs.ucr.edu>
Date:   Sun Jan 7 10:14:49 2018 -0800

set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <kho...@cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
 bc3139a8-67e5-0310-9ffc-ced21a209358


I can make your commit history look like this, but I’m not sure if all the 
changes in your code are reflected accurately. You might have to make sure 
manually, and see if your code and package work like you expect.

Once they work as expected, please don’t do anything with the commit history. 
Just add the new changes on top of what exists. It becomes extremely 
complicated and time taking to fix the commit history manually.

Best,

Nitesh


On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
wrote:

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE’s 
in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important.

Please wait for further instructions while we figure out how to resolve this 
issue.

Best,

Nitesh


On Jan 7, 2018, at 1:20 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

  I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our 
build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won’t show up in the release 
report.
Thanks

Nitesh


On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
wrote:

Hi Kevin,

I have your package reset to this commit 
e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new 
release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to 
Bioconductor.

Best,

Nitesh


On Jan 3, 2018, at 7:10 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

That sounds great, thanks.

Kev

Re: [Bioc-devel] git help

[Kevin Horan]

Nitesh,

Sorry, just saw your email now. You can go ahead and make those 
changes. Thanks for all your help.


Kevin


On 01/07/2018 11:22 AM, Turaga, Nitesh wrote:

Hi Kevin,

One last message, give me a green light to fix your repository once you have 
had a chance to see my emails.

Best,

Nitesh


On Jan 7, 2018, at 2:17 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
wrote:

Now your version numbers don’t match. You skip versions without those commits

Your history is supposed to look like this,

commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran <kho...@cs.ucr.edu>
Date:   Sun Jan 7 09:44:16 2018 -0800

History was rolled back 6 months to remove dup commits.
All changes since then are being re-applied in this one commit.

commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <kho...@cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
 bc3139a8-67e5-0310-9ffc-ced21a209358

##
Same for the RELEASE branch.
##

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran <kho...@cs.ucr.edu>
Date:   Sun Jan 7 10:14:49 2018 -0800

set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan <kho...@cs.ucr.edu>
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
 bc3139a8-67e5-0310-9ffc-ced21a209358


I can make your commit history look like this, but I’m not sure if all the 
changes in your code are reflected accurately. You might have to make sure 
manually, and see if your code and package work like you expect.

Once they work as expected, please don’t do anything with the commit history. 
Just add the new changes on top of what exists. It becomes extremely 
complicated and time taking to fix the commit history manually.

Best,

Nitesh


On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
wrote:

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE’s 
in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:52:08 2017 -0400

   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Hervé Pagès <hpa...@fredhutch.org>
Date:   Mon Oct 30 12:39:24 2017 -0400

   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important.

Please wait for further instructions while we figure out how to resolve this 
issue.

Best,

Nitesh


On Jan 7, 2018, at 1:20 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

  I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our 
build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won’t show up in the release 
report.
Thanks

Nitesh


On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
wrote:

Hi Kevin,

I have your package reset to this commit 
e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new 
release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to 
Bioconductor.

Best,

Nitesh


On Jan 3, 2018, at 7:10 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and 
put that repository up on our Git server.

 From that point onwards you’d have to reapply all the changes on that repository from 
"commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author

Re: [Bioc-devel] git help

[Kevin Horan]

Nitesh,

I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our 
build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won’t show up in the release 
report.
  
Thanks


Nitesh


On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
wrote:

Hi Kevin,

I have your package reset to this commit 
e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new 
release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to 
Bioconductor.

Best,

Nitesh


On Jan 3, 2018, at 7:10 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

   That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and 
put that repository up on our Git server.

 From that point onwards you’d have to reapply all the changes on that repository from 
"commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgi...@citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh





On Jan 3, 2018, at 4:28 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

   I tried to re-construct the repo starting from what is left in the SVN 
repository, but I couldn't get all the branches to come over and it just 
generally looks too different to easily replace the bioc repo.

   I was thinking though, if its easy for you to clobber the current bioc repo 
for ChemmineR and re-create it from the old SVN repo (ie, because you might 
have scripts from having done it the first time), then that might be an easier 
fix. Then I can check it out, apply the recent changes and push it back.

   But if you don't think that's a good idea, then I'll take your offer of help 
and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I’ll try to help you. I’ll take a look at your package and get back to you. 
Please forward this message to bioc-devel so that it’s public and other 
maintainers/users know that there is an issue with your package.

Best,

Nitesh


On Jan 3, 2018, at 2:31 PM, Kevin Horan <kho...@globalrecordings.net> wrote:

Nitesh,

   I am one of the maintainers for the ChemmineR package on bioconductor. I 
have a bad duplicate commit problem I was wondering if you could help me with. 
Basically, it seems one string of 1000 or so commits has been duplicated twice 
in the repository, so that there are now 3 copies of each of these commits. 
This mess is already in the bioconductor repository because in order to allow 
me to get some last minute changes in for the last release, someone at boic 
disabled the duplicate commit check for me. That was before I understood the 
extend of the problem.

   I'm not sure if its really your job to help with this sort of thing, as I 
understand that it's not a bioconductor problem. So if not that is fine. I've 
spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but 
I've only succeeded in make more duplicates. So I think I'd need to toss all 
the history up to the last release, which I image I'd need your help to reset 
the repo on the bioc side as well.

   If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan


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Re: [Bioc-devel] git help

[Kevin Horan]

Nitesh,

That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and 
put that repository up on our Git server.

 From that point onwards you’d have to reapply all the changes on that repository from 
"commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke <tgi...@citrus.ucr.edu>
Date:   Sat Aug 19 16:32:35 2017 -0700

 resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh





On Jan 3, 2018, at 4:28 PM, Kevin Horan <kho...@cs.ucr.edu> wrote:

Nitesh,

I tried to re-construct the repo starting from what is left in the SVN 
repository, but I couldn't get all the branches to come over and it just 
generally looks too different to easily replace the bioc repo.

I was thinking though, if its easy for you to clobber the current bioc repo 
for ChemmineR and re-create it from the old SVN repo (ie, because you might 
have scripts from having done it the first time), then that might be an easier 
fix. Then I can check it out, apply the recent changes and push it back.

But if you don't think that's a good idea, then I'll take your offer of 
help and we can try to figure out how to get rid of the duplicate commits. 
Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I’ll try to help you. I’ll take a look at your package and get back to you. 
Please forward this message to bioc-devel so that it’s public and other 
maintainers/users know that there is an issue with your package.

Best,

Nitesh


On Jan 3, 2018, at 2:31 PM, Kevin Horan <kho...@globalrecordings.net> wrote:

Nitesh,

I am one of the maintainers for the ChemmineR package on bioconductor. I 
have a bad duplicate commit problem I was wondering if you could help me with. 
Basically, it seems one string of 1000 or so commits has been duplicated twice 
in the repository, so that there are now 3 copies of each of these commits. 
This mess is already in the bioconductor repository because in order to allow 
me to get some last minute changes in for the last release, someone at boic 
disabled the duplicate commit check for me. That was before I understood the 
extend of the problem.

I'm not sure if its really your job to help with this sort of thing, as I 
understand that it's not a bioconductor problem. So if not that is fine. I've 
spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but 
I've only succeeded in make more duplicates. So I think I'd need to toss all 
the history up to the last release, which I image I'd need your help to reset 
the repo on the bioc side as well.

If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan



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Re: [Bioc-devel] git help

[Kevin Horan]

Nitesh,

I tried to re-construct the repo starting from what is left in the 
SVN repository, but I couldn't get all the branches to come over and it 
just generally looks too different to easily replace the bioc repo.


I was thinking though, if its easy for you to clobber the current 
bioc repo for ChemmineR and re-create it from the old SVN repo (ie, 
because you might have scripts from having done it the first time), then 
that might be an easier fix. Then I can check it out, apply the recent 
changes and push it back.


But if you don't think that's a good idea, then I'll take your 
offer of help and we can try to figure out how to get rid of the 
duplicate commits. Thanks.



Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I’ll try to help you. I’ll take a look at your package and get back to you. 
Please forward this message to bioc-devel so that it’s public and other 
maintainers/users know that there is an issue with your package.

Best,

Nitesh


On Jan 3, 2018, at 2:31 PM, Kevin Horan <kho...@globalrecordings.net> wrote:

Nitesh,

I am one of the maintainers for the ChemmineR package on bioconductor. I 
have a bad duplicate commit problem I was wondering if you could help me with. 
Basically, it seems one string of 1000 or so commits has been duplicated twice 
in the repository, so that there are now 3 copies of each of these commits. 
This mess is already in the bioconductor repository because in order to allow 
me to get some last minute changes in for the last release, someone at boic 
disabled the duplicate commit check for me. That was before I understood the 
extend of the problem.

I'm not sure if its really your job to help with this sort of thing, as I 
understand that it's not a bioconductor problem. So if not that is fine. I've 
spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but 
I've only succeeded in make more duplicates. So I think I'd need to toss all 
the history up to the last release, which I image I'd need your help to reset 
the repo on the bioc side as well.

If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan




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[Bioc-devel] openbabel 2.4.1

[Kevin Horan]

The package ChemmineOB depends on the external library OpenBabel. There 
is now a new version of it, version 2.4.1. Could you please install this 
on all three operating systems (just for devel )? You can find general 
OpenBabel build instructions here 
, and ChemmineOB 
specific instructions in the INSTALL file.
 On the mac, it should work with libc++ now (previously it only 
worked with libstdc++), so don't force it use libstd++ anymore (unless 
you have other reasons for doing so, in which case just let me know so I 
can adjust the make file). No special CMAKE flags should be necessary.

Thanks.

Kevin

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[Bioc-devel] disable windows build for EiR development

[Kevin Horan]

Can you please disable the windows build for eiR in the development 
branch? Thanks.


Kevin Horan

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Re: [Rd] using openbabel plugins in R

[Kevin Horan]

After some more testing I have found that it actually does work if I 
compile without the plugin library but load it with dyn.load. I'm not 
sure why this wasn't working before. It only works though if the plugin 
library is loaded before libobtest2.so (the open babel main lib basically).

So, to clarify, the following works now:

g++ -shared -o libobtest2.so obtest2.o -fpic -lopenbabel -lR

Rdyn.load(/usr/lib/openbabel/2.2.3/mdlformat.so)
Rdyn.load(libobtest2.so)
R.Call(test)
  format: 0x7fe114c96d20  #this is the correct result
  NULL


But now I have a chicken and egg problem. The plugin libraries are 
not stored in a standard directory, but open babel provides a function 
to list their paths. So I need to load the open babel library to fetch 
the plugin paths, then I can load the plugins, but, oops, too late, the 
open babel library is already loaded so loading the plugins now doesn't 
work. I tried using dyn.unload(libobtest2.so) but it didn't work. It 
seems like I'd have to compile a small executable program that uses 
openbabel to fetch the plugin paths, then run it as an external program 
from within R, then load the plugins, then load the open babel lib.
Does it make any sense that the order in which these are loaded 
affects things? Is there a way to load the plugin lib later and still 
have  it work? If the order does have to be maintained, any better ideas 
how to accomplish this? Thanks.

Also, here is the dlopen command that openbabel uses:
dlopen(lib_name.c_str(), RTLD_LAZY | RTLD_GLOBAL)


Kevin


On 03/26/2013 06:54 AM, Dirk Eddelbuettel wrote:

On 25 March 2013 at 12:50, Kevin Horan wrote:
| I posted this in openbabel-devel but didn't get much help, so hopefully
| someone here can help. I don't think its too openbabel specific.
|
| I would like to make use of open babel from within the R language.
| Initially I just need to do some format conversions, but may expand the
| usage to other parts of OpenBabel as well. I am familiar with embedding
| C/C++ code in R, but I'm having some trouble with the plugin mechanism
| of OpenBabel in this case. The  problem is that the formats are not
| available when I run the OpenBabel code from within R. So, for example,
| if I search for the SDF format like so:
|   OBFormat *format = conv.FindFormat(SDF);

[...]

|  The way it works normally in OpenBabel is that each plugin is its
| own shared library and then they get loaded at run time with the dlopen
| function (on linux at least). I have verified that this code is still
| being executed when called from within R, but it doesn't work for some
| reason.

I would try to start from the smallest possible working examples.  R itself
uses dlopen (see eg $RHOME/modules/ for the files it loads), and so does
OpenBabel. Maybe some wires get crossed. You may well have to dig down with
the debugger and see what assumptions / environment variables / ... are valid
or invalid between the working and non-working case.

Dirk



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Re: [Rd] using openbabel plugins in R

[Kevin Horan]

Thanks for all the suggestions. I have discovered that the problem is 
fixed in openbabel 2.3.x. I had actually been testing with open babel 
2.3.2 (as well as 2.2.3), but I was running it from the build directory 
since I didn't want to install it on the system as I was only testing 
with it. Because of this, 2.3.2 failed in the same way as 2.2.3 (the 
version actually installed), but for a different reason (It couldn't 
find the modules directory ). Actually installing 2.3.2 fixed the problem.


Kevin

On 03/27/2013 11:20 AM, Simon Urbanek wrote:

On Mar 27, 2013, at 1:02 PM, Kevin Horan wrote:


After some more testing I have found that it actually does work if I compile 
without the plugin library but load it with dyn.load. I'm not sure why this 
wasn't working before. It only works though if the plugin library is loaded 
before libobtest2.so (the open babel main lib basically).
So, to clarify, the following works now:

g++ -shared -o libobtest2.so obtest2.o -fpic -lopenbabel -lR

Rdyn.load(/usr/lib/openbabel/2.2.3/mdlformat.so)
Rdyn.load(libobtest2.so)
R.Call(test)
  format: 0x7fe114c96d20  #this is the correct result
  NULL


But now I have a chicken and egg problem.

Run the egg in a separate R process (i.e. use system() to call another R 
process which loads libobtest2.so and calls the API to get the path). Then load 
the modules followed by the .so.

Note that all this is inherently fragile and probably not portable (e.g. it 
seems to assume flat namespaces). Another way (only slightly less fragile) is 
to link libobtest2.so against the modules directly.

The real issue seems in openbabel - there is really no reason why it shouldn't 
be loading the modules. I didn't look at it, but it could be that it is simply 
trying to detect things in the wrong namespace and thus mis-detecting something 
in R as its own. It's obviously a bad design in openbabel as it's polluting the 
global namespace, but that's another story... (Linux users won't notice as 
Linux doesn't support two-level namespaces AFAIK).

Cheers,
Simon



The plugin libraries are not stored in a standard directory, but open babel provides a 
function to list their paths. So I need to load the open babel library to fetch the 
plugin paths, then I can load the plugins, but, oops, too late, the open babel library is 
already loaded so loading the plugins now doesn't work. I tried using 
dyn.unload(libobtest2.so) but it didn't work. It seems like I'd have to 
compile a small executable program that uses openbabel to fetch the plugin paths, then 
run it as an external program from within R, then load the plugins, then load the open 
babel lib.
Does it make any sense that the order in which these are loaded affects 
things? Is there a way to load the plugin lib later and still have  it work? If 
the order does have to be maintained, any better ideas how to accomplish this? 
Thanks.
Also, here is the dlopen command that openbabel uses:
dlopen(lib_name.c_str(), RTLD_LAZY | RTLD_GLOBAL)


Kevin


On 03/26/2013 06:54 AM, Dirk Eddelbuettel wrote:

On 25 March 2013 at 12:50, Kevin Horan wrote:
| I posted this in openbabel-devel but didn't get much help, so hopefully
| someone here can help. I don't think its too openbabel specific.
|
| I would like to make use of open babel from within the R language.
| Initially I just need to do some format conversions, but may expand the
| usage to other parts of OpenBabel as well. I am familiar with embedding
| C/C++ code in R, but I'm having some trouble with the plugin mechanism
| of OpenBabel in this case. The  problem is that the formats are not
| available when I run the OpenBabel code from within R. So, for example,
| if I search for the SDF format like so:
|   OBFormat *format = conv.FindFormat(SDF);

[...]

|  The way it works normally in OpenBabel is that each plugin is its
| own shared library and then they get loaded at run time with the dlopen
| function (on linux at least). I have verified that this code is still
| being executed when called from within R, but it doesn't work for some
| reason.

I would try to start from the smallest possible working examples.  R itself
uses dlopen (see eg $RHOME/modules/ for the files it loads), and so does
OpenBabel. Maybe some wires get crossed. You may well have to dig down with
the debugger and see what assumptions / environment variables / ... are valid
or invalid between the working and non-working case.

Dirk


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[Rd] using openbabel plugins in R

[Kevin Horan]

I posted this in openbabel-devel but didn't get much help, so hopefully 
someone here can help. I don't think its too openbabel specific.


I would like to make use of open babel from within the R language.
Initially I just need to do some format conversions, but may expand the
usage to other parts of OpenBabel as well. I am familiar with embedding
C/C++ code in R, but I'm having some trouble with the plugin mechanism
of OpenBabel in this case. The  problem is that the formats are not
available when I run the OpenBabel code from within R. So, for example,
if I search for the SDF format like so:
 OBFormat *format = conv.FindFormat(SDF);
I always get back a 0 value. The same chunk of code executed outside of
R, as a normal stand-alone program, works fine. So does anyone know how
I can ensure that the formats get loaded? Thanks.
 One other thing to mention, someone might suggest linking against a
static version of openbabel which includes all the plugins. I would like
to avoid that if possible since this needs to work in an R package that
will be distributed across platforms, so it would be hard to ask people
to compile a special, static, version of openbabel just to compile this
R package. Since it needs to work on windows, mac and linux, it would be
nice  if I can make use of any existing installed shared obenbabel
libraries. If it turns out it can't be done, then I'll go down that
path. Thanks.

 Here is an example of the problem:

test program (obtest2.cc):

#include iostream
#include openbabel/obconversion.h
#include R.h
#include Rinternals.h

extern C {   SEXP test(); }

int main(){
test();
}
SEXP  test()
{
OpenBabel::OBConversion conv;
OpenBabel::OBFormat *format = conv.FindFormat(SDF);   //
search for SDF format
std::coutformat: formatstd::endl;// print out 
search result, either 0   or an address

return R_NilValue;
}


compile:
 g++  -I/usr/include/openbabel-2.0 -I/usr/share/R/include -fpic -c 
obtest2.cc -o obtest2.o
 g++ -o obtest2 obtest2.o -fpic  -lopenbabel 
-lR   # Executable
 g++ -shared -o libobtest2.so obtest2.o -fpic  -lopenbabel -lR  # R 
library


Run executable:
 $ ./obtest2
 format: 0x7f1858275d20  #found some result, this is what I expect

Run in R:
 Rdyn.load(libobtest2.so)
 R.Call(test)
 format: 0  # the format was not found, so 0 was
returned
 NULL


After some more experimentation, I have discovered I can get it to work 
in the following way, but I think it is a bit impractical. If I compile 
the shared library as:
g++ -shared -o libobtest2.so obtest2.o -fpic 
/usr/lib/openbabel/2.2.3/mdlformat.so -lopenbabel -lR

so the name of one of the plugins is specified. Then, in R I run:

Rdyn.load(/usr/lib/openbabel/2.2.3/mdlformat.so)
Rdyn.load(libobtest2.so)
R.Call(test)
format: 0x7fe114c96d20
NULL
So then it works. But this requires that I know the full path to every 
plugin when the code is compiled and when the library is loaded. Is 
there a practical way to do this, say, if this were part of an R 
package? I have also tried compiling the shared library as before, 
without the plugin, and then just loading the plugin with dyn.load but 
this does not work. It seems like it should though, does anyone know why 
it doesn't? Conversely, if you compile with the plugin specified, but 
don't load it with dyn.load it seg faults.
The way it works normally in OpenBabel is that each plugin is its 
own shared library and then they get loaded at run time with the dlopen 
function (on linux at least). I have verified that this code is still 
being executed when called from within R, but it doesn't work for some 
reason.

Also, swig does not help.

Thanks.

Kevin

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[Rd] compiling C code using headers from another R package

[Kevin Horan]

I am developing an R package, eiR,  which depends on another C library, 
GNU scientific library (GSL). In order to make life easier for the user, 
it would be nice to not have this as an external dependency, thus I 
would like to wrap this library in another R package, say GSLR for 
example. Thus far I know how to do this. The C code in eiR requires the 
.so library and the header files from GSL in order to compile. So the 
idea is that eiR would depend on GSLR, then GSLR gets compiled and 
installed first, then, while eiR is installing, it should be able to 
make use of the GSL library and header files while compiling. So my 
question is, how do I know where the GSL library and header files, 
packaged in GSLR, would live so I can point the compiler at them? I know 
how to find the installed directory of an R package from within R, but 
is there way to find that out using just Makevars or a Makefile? I'm 
open to suggestions about a better way organize all of this as well. I 
like the idea of keeping the GSL code separate so that it can be 
updated/changed independently from eiR though.
I'm also aware of the gsl R library on CRAN, however, this just 
wraps GSL in R functions, but I need to use the GSL C functions in other 
C code in eiR.


Thanks.

Kevin

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[Rd] compiling C code using headers from another R package

[Kevin Horan]

Thanks for your input. To clarify, I don't need to use any part of 
GSL in my R code, nor do I wish to make any part of it accessible to 
users of eiR. I need it to compile other C/C++ code (LSH KIT), which I 
did not write, that will itself be used in eiR.
My goal is allow the user to install eiR without also having to 
install GSL before hand. The target audience is people in bioinformatics 
who may not how to install something like GSL. It seems like what I was 
suggesting is not such a good idea, if it will be hard to reliably find 
the header files from another R package. I could also push all of GSL 
into eiR, but as GSL has over 5000 files, this makes the package very 
large ( 22 MB) and  slow to compile. Both of which are a problem when 
submitting a package to bioconductor. It may very well be that leaving 
GSL as an external dependency to eiR is really the best and easiest way, 
but I just wanted to see if there was any way to make it easier for the 
user. So, any other suggestions about how this could be accomplished?  
Thanks.


Kevin

On 03/12/2013 05:26 AM, Simon Urbanek wrote:

Kevin,

On Mar 11, 2013, at 5:20 PM, Kevin Horan wrote:


I am developing an R package, eiR,  which depends on another C library, GNU 
scientific library (GSL). In order to make life easier for the user, it would 
be nice to not have this as an external dependency, thus I would like to wrap 
this library in another R package, say GSLR for example. Thus far I know how to 
do this. The C code in eiR requires the .so library and the header files from 
GSL in order to compile. So the idea is that eiR would depend on GSLR, then 
GSLR gets compiled and installed first, then, while eiR is installing, it 
should be able to make use of the GSL library and header files while compiling. 
So my question is, how do I know where the GSL library and header files, 
packaged in GSLR, would live so I can point the compiler at them? I know how to 
find the installed directory of an R package from within R, but is there way to 
find that out using just Makevars or a Makefile? I'm open to suggestions about 
a better way organize all of this as well. I like the !

idea of keeping the GSL code separate so that it can be updated/changed 
independently from eiR though.

Have a look at Rcpp.



I'm also aware of the gsl R library on CRAN, however, this just wraps GSL 
in R functions, but I need to use the GSL C functions in other C code in eiR.


Why is what you are proposing any better than simply using GSL in eiR? You will 
still need the GSL external dependency for GSLR and you are only adding a lot 
of complexity by linking into another package's external directory (you cannot 
use libs) which is in itself very tricky (you'll have to deal with both static 
and shared version, multi-arch setups, possible relocation etc.). It won't make 
it any easier on the user, rather to the contrary as there will be more things 
to break. The only reason Rcpp goes into such length to do this is because it 
has no choice (the Rcpp library has to use the same libR so cannot be used as 
external dependency) - I would certainly not recommend it for something as 
trivial as providing GSL.

Cheers,
Simon



Thanks.

Kevin

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Re: [Rd] compiling C code using headers from another R package

[Kevin Horan]

On 03/12/2013 09:55 AM, Simon Urbanek wrote:

On Mar 12, 2013, at 12:30 PM, Kevin Horan wrote:


Thanks for your input. To clarify, I don't need to use any part of GSL in 
my R code, nor do I wish to make any part of it accessible to users of eiR. I 
need it to compile other C/C++ code (LSH KIT), which I did not write, that will 
itself be used in eiR.
My goal is allow the user to install eiR without also having to install GSL 
before hand.

If your package is on CRAN they won't need to as we are providing Mac and 
Windows binaries. Linux can get the binaries form their distro, so the 
dependencies are installed automatically.
It will (hopefully) be hosted on BioConductor. I suppose they would do 
the same thing? I didn't realize this was the normal case.




The target audience is people in bioinformatics who may not how to install 
something like GSL. It seems like what I was suggesting is not such a good idea, 
if it will be hard to reliably find the header files from another R package. I 
could also push all of GSL into eiR, but as GSL has over 5000 files, this makes 
the package very large (22 MB) and  slow to compile. Both of which are a 
problem when submitting a package to bioconductor. It may very well be that 
leaving GSL as an external dependency to eiR is really the best and easiest way, 
but I just wanted to see if there was any way to make it easier for the user.

Can you clarify what you mean by user? The vast majority of R users use 
binaries, so all this is irrelevant to them as they don't need to install GSL at all.
I just mean biologists installing and using the package. I didn't 
realize they are always distributed in binary form, guess I've had my 
head stuck in the linux world for too long :).


Cheers,
Simon



So, any other suggestions about how this could be accomplished?  Thanks.

Kevin

On 03/12/2013 05:26 AM, Simon Urbanek wrote:

Kevin,

On Mar 11, 2013, at 5:20 PM, Kevin Horan wrote:


I am developing an R package, eiR,  which depends on another C library, GNU 
scientific library (GSL). In order to make life easier for the user, it would 
be nice to not have this as an external dependency, thus I would like to wrap 
this library in another R package, say GSLR for example. Thus far I know how to 
do this. The C code in eiR requires the .so library and the header files from 
GSL in order to compile. So the idea is that eiR would depend on GSLR, then 
GSLR gets compiled and installed first, then, while eiR is installing, it 
should be able to make use of the GSL library and header files while compiling. 
So my question is, how do I know where the GSL library and header files, 
packaged in GSLR, would live so I can point the compiler at them? I know how to 
find the installed directory of an R package from within R, but is there way to 
find that out using just Makevars or a Makefile? I'm open to suggestions about 
a better way organize all of this as well. I like th!

e idea of keeping the GSL code separate so that it can be updated/changed 
independently from eiR though.

Have a look at Rcpp.



I'm also aware of the gsl R library on CRAN, however, this just wraps GSL 
in R functions, but I need to use the GSL C functions in other C code in eiR.


Why is what you are proposing any better than simply using GSL in eiR? You will 
still need the GSL external dependency for GSLR and you are only adding a lot 
of complexity by linking into another package's external directory (you cannot 
use libs) which is in itself very tricky (you'll have to deal with both static 
and shared version, multi-arch setups, possible relocation etc.). It won't make 
it any easier on the user, rather to the contrary as there will be more things 
to break. The only reason Rcpp goes into such length to do this is because it 
has no choice (the Rcpp library has to use the same libR so cannot be used as 
external dependency) - I would certainly not recommend it for something as 
trivial as providing GSL.

Cheers,
Simon



Thanks.

Kevin

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