Skip to content

[Bioc-devel] rsvg on mac

4 messages · Kevin Horan, Obenchain, Valerie

Original
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:

  
  


  


    

    

      
      

        


  

        

      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 <Valerie.Obenchain at roswellpark.org<mailto:Valerie.Obenchain at 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 <Valerie.Obenchain at roswellpark.org<mailto:Valerie.Obenchain at 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

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org><mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at 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.

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at 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.

  
  


  


      

    

    
4 days later

    

      
      

        


  

        

      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:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      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 <Valerie.Obenchain at roswellpark.org<mailto:Valerie.Obenchain at 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 <Valerie.Obenchain at roswellpark.org<mailto:Valerie.Obenchain at 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

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org><mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at 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.

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at 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.




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.