[Bioc-devel] xps build problem on veracruz2

Fri Mar 24 18:02:18 CET 2017

On 03/24/2017 06:52 AM, cstrato wrote:
> R/Bioc is still building on Mavericks,

Not for R devel (3.4). The R folks have switched to El Capitan a few
days ago:

   https://r.research.att.com/

> and before was built on Snow
> Leopard (which many people are sill using).
>
> Personally I think that it does not make much difference whether
> Mavericks or El Capitan (or Yosemite) is used to build R/Bioc.

How much experience you have with setting a Mavericks or El Capitan
build machine to build and distribute thousands of package binaries for
hundreds ot thousands of users?

>
> However, Sierra is different, and when the CRAN people are experimenting
> with clang 4.0.0 for producing the Mac binaries, as Herve has mentioned,
> then backwards-compatibility would probably be lost anyhow.

I think you misunderstood what Dan said. Backward-compatibility is
always lost i.e. binaries built on a given OS X versions are not
guaranteed to be backward compatible with older OS X versions. That's
why building them on the latest OS X version is a bad idea.

>
> But I understand that this is a decision the CRAN people have to make.

You're welcome to discuss this choice on the R-SIG-Mac mailing list.

Cheers,
H.

>
> Best regards,
> Christian
>
>
> On 03/24/17 01:10, Dan Tenenbaum wrote:
>>
>>
>> ----- Original Message -----
>>> From: "Hervé Pagès" <hpages at fredhutch.org>
>>> To: "cstrato" <cstrato at aon.at>, "bioc-devel" <bioc-devel at r-project.org>
>>> Sent: Thursday, March 23, 2017 12:14:38 PM
>>> Subject: Re: [Bioc-devel] xps build problem on veracruz2
>>
>>> On 03/23/2017 11:09 AM, cstrato wrote:
>>>> Dear Herve,
>>>>
>>>> Thank you for your explanation.
>>>>
>>>> The reason that xps does not work with ROOT 6 is that I have tried it
>>>> but there seem to be so many changes, that I did not succeed.
>>>> Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5
>>>> was still supported, I have decided to stay with ROOT 5.
>>>
>>> OK
>>>
>>>>
>>>> BTW, I have also one question:
>>>> Why did you decide to set up a new Mac with El Capitan instead of using
>>>> the newest OS Sierra? (I have the impression that most Mac users are
>>>> either happy to stay with their old OS or they upgrade to the newest
>>>> one.)
>>>
>>> Same reason as for the choice of compilers: that's what the R folks
>>> decided to use for producing the Mac binaries of R and CRAN packages.
>>> We're just following their lead on that.
>>>
>>
>> Also, it's always good not to require users to upgrade if they don't
>> have to. Building on El Capitan means users will not have to upgrade
>> to macOS Sierra if they don't want to. Building on Sierra would mean R
>> and packages would not be backwards-compatible with El Capitan.
>>
>> But it's a tradeoff that also involves the difficulty of maintaining
>> build machines with old OSes, and wanting to take advantage of newer
>> compiler technology. Otherwise R/Bioc would still be building on
>> Mavericks, or Snow Leopard...
>>
>> Dan
>>
>>
>>> Cheers,
>>> H.
>>>
>>>>
>>>> Best regards,
>>>> Christian
>>>>
>>>>
>>>> On 03/23/17 17:47, Hervé Pagès wrote:
>>>>> Hi Christian,
>>>>>
>>>>> The CRAN folks are currently experimenting with clang 4.0.0 for
>>>>> producing the Mac binaries of R and CRAN packages so we are using
>>>>> the same on veracruz2. This is a version of clang that is ahead of
>>>>> what's in XCode 8.x or XCode 7.x. So I guess that means we'll have
>>>>> to compile ROOT from source on veracruz2.
>>>>>
>>>>> BTW any reason not to make xps work with ROOT 6?
>>>>>
>>>>> Cheers,
>>>>> H.
>>>>>
>>>>> On 03/23/2017 07:28 AM, cstrato wrote:
>>>>>> Dear Valerie,
>>>>>>
>>>>>> I have seen that you have set up a new Mac server, veracruz2,
>>>>>> running El
>>>>>> Capitan.
>>>>>>
>>>>>> Although the development version of xps does even run on Mac OS
>>>>>> Sierra,
>>>>>> one issue still remains the same:
>>>>>>
>>>>>> You need to install the latest ROOT version 5, since xps does not run
>>>>>> with ROOT 6!
>>>>>>
>>>>>> So you need to install on veracruz2 the same root version that you
>>>>>> have
>>>>>> installed on toluca2 running Maverics, i.e.
>>>>>> root_v5.34.36.macosx64-10.11-clang70.dmg
>>>>>>
>>>>>> However, if you have installed on El Capitan XCode 8.x instead of
>>>>>> XCode
>>>>>> 7.x, then you need to compile ROOT from source, i.e.:
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e=
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> The README file of xps does explain how to compile ROOT for
>>>>>> Sierra. This
>>>>>> should also be valid for El Capitan running XCode 8.x.
>>>>>>
>>>>>> Thank you in advance.
>>>>>> Best regards,
>>>>>> Christian
>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>>>>>> V.i.e.n.n.a           A.u.s.t.r.i.a
>>>>>> e.m.a.i.l:        cstrato at aon.at
>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&e=
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fredhutch.org
>>> Phone:  (206) 667-5791
>>> Fax:    (206) 667-1319
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e=
>>>
>>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319