[Bioc-devel] rsvg on mac

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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