Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

Yes, when a new version appears on CRAN it is automatically picked up by the 
build machines.

Valerie


 On 05/14/2018 05:04 AM, Kevin Horan wrote:

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 
> 
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

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 
> 
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

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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 
>>> >> > 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
>>> 
>>>
>>> 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
 > 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

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Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

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 
> 
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

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 
> 
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

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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 
>  > 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
> 
>
> 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
>> > > 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
>>
>> ___
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>>
>>
>>
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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

[Alexey Sergushichev]

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> 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
>
> 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  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
>>
>> 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
>>
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>>
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Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

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

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 
> 
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

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Re: [Bioc-devel] rsvg on mac

[Alexey Sergushichev]

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> 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
>
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>
>
>
>
>
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Re: [Bioc-devel] rsvg on mac

[Hervé Pagès]

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

 ___
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>>>
>>>
>>> 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 
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Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

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

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email message is prohibited. If you have received this message in error, please 
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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
>>
>> ___
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>>
>
>
> This email message may contain legally privileged and/or confidential 
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> or agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
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> received this message in error, please notify the sender immediately 
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Re: [Bioc-devel] rsvg on mac

[Obenchain, Valerie]

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

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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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