[Bioc-devel] xps build problem on veracruz2

Hervé Pagès hpages at fredhutch.org
Fri Mar 24 19:23:47 CET 2017 

On 03/24/2017 11:10 AM, cstrato wrote:
>
>
> On 03/24/17 18:02, Hervé Pagès wrote:
>> 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:
>>
>
> You are right, I did not check R devel.
>
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__r.research.att.com_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=aV7U6Qu8HkkL9dhD7thXz2c2geZd1KmfWnoZkiyu6hs&s=EDYb8eN2bAg_TtTfDURARDLiz4AoKggk2QLfABIdxTA&e=
>>
>>> 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?
>>
>
> You probably misunderstood what I wanted to say.
>
> It is clear to me that you are doing a great job distributing thousands
> of package binaries. No one does know it better than me with the special
> problems you have to build binaries for xps. I really appreciate that
> during all these years you and Dan (and others) managed to support xps
> like all other BioC packages.
>
> I meant that from the user standpoint it probably does not matter much
> which of these three systems are used to build BioC, in contrast to Sierra.

Of course it matters. If you use an older OS than the one we use to
produce the binaries then some binaries won't work for you. You keep
missing the whole point.

H.

>
> But as you said below backward-compatibility is always lost, so the
> question which system to use to build R/BioC is always tricky. Maybe,
> the best (?) decision would be to use the system which most Mac users
> are currently using, but I don't know.
>
> Best regards,
> Christian
>
>>>
>>> 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

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