[Bioc-devel] xps build problem on veracruz2

cstrato cstrato at aon.at
Fri Mar 24 20:14:36 CET 2017 


On 03/24/17 19:55, Hervé Pagès wrote:
> On 03/24/2017 11:37 AM, cstrato wrote:
>>
>>
>> On 03/24/17 19:23, Hervé Pagès wrote:
>>> 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.
>>>
>>
>> Sorry, but I do understand this point. Users who are still using e.g.
>> Snow Leopard (because they think this was the best system) will have
>> problems. For that reason I thought that maybe it is best to use the
>> system which is currently used by most users.
>
> That would be the thing to do if we didn't have neither forward- nor
> backward- compatibility. But we *do* have forward-compatibility. So
> there is no reason to use the system which is currently used by most
> users. It's enough to make sure that we use a system that is
> *compatible* with what most users have. And also not too old because
> it's hard to find powerful hardware that runs old OS X versions and
> because many software components needed for the builds are not
> available or not maintained anymore for old OS X versions.
>
> Like Dan said, it's a tradeoff.
>
> H.
>

You are right, using a system which is compatible with what most users 
have, is the best choice.

Christian

>
>>
>> Christian
>>
>>
>>>>
>>>> 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=
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>
>>>
>

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