[Bioc-devel] rsvg on mac

Wed Feb 21 18:43:42 CET 2018

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&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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>>>>>>
>>>>>>
>>>>>
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