[Bioc-devel] rsvg on mac

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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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

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 
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is prohibited. If you have received this message in error, please 
notify the sender immediately by e-mail and delete this email 
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This email message may contain legally privileged and/or confidential 
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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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w&e=

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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=7UDK9omF9qsdLzWH6wEh_fyNE5BuQbNbJzc0v925ElE&e=), 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w&e=

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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=B43U-waIixUyD4yJS4OySSIX5jVaAXp98jUM348m8oU&e=


Kevin

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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

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 <Valerie.Obenchain@
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

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.

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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w&e= 


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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=7UDK9omF9qsdLzWH6wEh_fyNE5BuQbNbJzc0v925ElE&e=), 
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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w&e= 


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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=B43U-waIixUyD4yJS4OySSIX5jVaAXp98jUM348m8oU&e= 



Kevin

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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