[Bioc-devel] xps build problem on veracruz2

On 03/24/17 19:55, Herv? Pag?s wrote:

On 03/24/2017 11:37 AM, cstrato wrote:

On 03/24/17 19:23, Herv? Pag?s wrote:

On 03/24/2017 11:10 AM, cstrato wrote:

On 03/24/17 18:02, Herv? Pag?s 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: "Herv? Pag?s" <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, Herv? Pag?s 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
_._._._._._._._._._._._._._._._._._

--
Herv? Pag?s

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