[Bioc-devel] xps build problem on veracruz2

Hervé Pagès hpages at fredhutch.org
Fri Mar 24 19:55:23 CET 2017 

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.


>
> 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=
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>

-- 
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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