Dear Prof. Ripley,
Thank you for this extensive information.
You mention that you have been working hard on making R and CRAN
packages installable using clang, which is quite an effort.
Currently, the Bioconductor maintainers are doing the same, i.e.
checking which BioC packages are installable using clang, and I was
informed that my package 'xps' cannot be installed using clang.
In my case the main problem seems to be that the version of clang used
has a bug which prevents compilation of xps (and the necessary ROOT C++
framework).
Concretely, both the Bioconductor server running Snow Leopard and my
Snow Leopard Mac have versions of Xcode, which include clang Version
3.0. In order to compile ROOT successfully, at least clang Version 3.1
is necessary, see:
http://root.cern.ch/phpBB3/viewtopic.php?f=3&t=14614#p62969
On my Mac running Lion (10.7.5) I have currently also installed Xcode
4.2.1 which contains clang Version 3.0, so I could reproduce this error
also on Lion. After downloading the the 'Command Line Tools (OS X Lion)
for Xcode - March 2013' from the Apple developer site the version of
clang is now:
$ clang -v
Apple LLVM version 4.2 (clang-425.0.27) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin11.4.2
Using this version I could successfully compile both ROOT and xps. The
problem is that I do not know how to obtain a more recent version of
clang for Snow Leopard, the system currently running on the BioC server.
I would very much appreciate if you could propose a solution for this
problem.
Thank you in advance.
Best regards,
Christian
On 4/18/13 11:03 AM, Prof Brian Ripley wrote:
> Since I have heard that R and Bioconductor packages should in the future
> be built with clang since Apple will be discontinuing support of gcc, my
> question is:
I've not heard that, and you give no reference. It's a pretty safe
prediction except for timing: it could be a year away. So your
questions are not relevant until it is announced. The documentation in
the current R manuals is currently the correct advice.
Apple have announced the imminent discontinuation of llvm-gcc, and we
take that to mean it will not be in Xcode 4.7 (or 5.0 if that is
released first). That would mean that once that is released, for most
users of Lion and later llvm-gcc will disappear (as most users will get
an automatic upgrade from the AppStore, or as in my case, the sysadmins
will push out an update).
So we have been working hard on making R and CRAN packages installable
using clang (there were too many problems at decision time for 3.0.0).
How to switch a CRAN binary installation to use clang[++] is in the R >=
3.0.0 manuals. That may not work for packages with configure scripts:
for that you may need R-patched.
There are now only seven CRAN packages which have bugs which stop
installation under clang, and all the maintainers have been sent
patches. (Two of those do not install under gcc 4.8.0 either.)
Very likely at some point Simon will switch the CRAN binary distribution
to use clang, but the real point is that many end-users will need to do
so soon.
Given that R 3.0.0 supports OS 10.6 (Snow Leopard), it is likely that we
will do so for all of the 3.0.x series, even though 10.6 will almost
certainly reach end-of-life well before 3.1.0 is due. In that case the
CRAN builder could stick with llvm-gcc for that series, but it may prove
more convenient for end-users to switch to the distribution to clang
before then. Only time will tell.
On 17/04/2013 18:45, cstrato wrote:
Dear Prof. Ripley, dear Simon,
Thank you for this information about Xcode and CLTs.
Since I have heard that R and Bioconductor packages should in the future
be built with clang since Apple will be discontinuing support of gcc, my
question is:
- Which version of Xcode and/or CLTs should Snow Leopard users install
in the future? (the last official version for Snow Leopard is
xcode_3.2.6)
- Which version of Xcode and/or CLTs should Lion/Mountain Lion users
install so that they can still compile their packages with gcc, too?
(the current version is xcode_4.6.2)
From the discussion I understand that it is no longer necessary to
install Xcode at all, installing CLTs is sufficient. Is this correct?
Best regards,
Christian
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