[Bioc-devel] Installing pkg with configure with support to multiple architectures
Hi Steve,
It's the CRAN build... and it behaves as expected, as long as the
package does not have a configure script (I should make it clear that
I always install packages from the source, ie, install.packages(...,
type='source') ).
For example, Biobase does not have a configure script. Then:
biocLite('Biobase')
gives me:
* installing *source* package ?Biobase? ...
** libs
*** arch - i386
<bunch of stuff>
*** arch - x86_64
<another bunch>
* DONE (Biobase)
Now, affyio and affy have a configure script:
biocLite(c('affyio', 'affy'))
gives me:
* installing *source* package ?affyio? ...
<./configure output>
** libs
*** arch - x86_64
<bunch of stuff>
* DONE (affyio)
* installing *source* package ?affy? ...
<./configure output>
** libs
*** arch - x86_64
<bunch of stuff>
* DONE (affy)
Note that affyio and affy were not installed under i386.
Now, try to install gcrma (has C code, but doesn't have a configure:
biocLite('gcrma')
gives:
* installing *source* package ?gcrma? ...
** libs
*** arch - i386
<bunch of stuff>
*** arch - x86_64
<bunch of stuff>
*** arch - i386
Error : package ?affy? is not installed for 'arch=i386'
Error: loading failed
Execution halted
*** arch - x86_64
ERROR: loading failed for ?i386?
* removing ?/Users/carval03/Rlibs/2.14/gcrma?
So, to get this to work, I need to download the tar.gz files and do
R --arch x86_64 CMD INSTALL pkg_version.tar.gz
R --arch i386 CMD INSTALL --libs-only pkg_version.tar.gz
for pkg = affyio, affy
and I was wondering if there was an automagic way of doing this
(which, I'd hopefully bring to oligo as well).
b
On 27 January 2012 14:36, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
Hi, Speaking for R-on-mac -- Isn't a multi-arch build the default as long as your R was compiled as multi-arch? For instance, if I try to source compile any packge (w/ c code) using a "release" version of R (d/l'd from CRAN), it will by default compile the package for x86_64 and i386, unless I specify `R CMD INSTALL --no-multiarch` Now, if I'm compiling the same package using a my own source-compiled version of R (which is only compiled as 64 bit), then it won't build the i386 version of the package. So, I guess my question is if this behavior you are seeing is when using an R you built yourself, or is it an official CRAN build? If it's the official build, I'd also be confused as to how some package were built w/o being multiarch (unless you specifically asked them to be built that way). HTH, -steve On Fri, Jan 27, 2012 at 8:29 AM, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
Thanks Dan and Martin, Dan, yes, your assumption is correct (I'm trying to do this on a Mac). The major problem (actually, annoyance) for me is when something like the following happens (running R under x86_64 and installing via install.packages/biocLite): - Install pkg1, which has a configure script... Then, pkg1 is installed under x86_64; - (try to) install pkg2, which does not have a configure script, but depends on pkg1.... it installs the x86_64 part just fine, but the i386 fails (because pkg1 isnt available under i386)... then the whole installation of pkg2 fails. Maybe it's just something basic I'm missing from my end? b On 26 January 2012 21:49, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
On Thu, Jan 26, 2012 at 12:45 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
On 01/26/2012 06:01 AM, Benilton Carvalho wrote:
A package with a configure file is installed only on the architecture that called the install script. So I need to, manually, do: R --arch x86_64 CMD INSTALL oligo_version.tar.gz R --arch i386 CMD INSTALL --libs-only oligo_version.tar.gz Is there anything I can add to the package in order to automate this?
Hi Benilton -- on a not-quite-current R-devel, I have
R CMD INSTALL --help
... and on Windows only ? ? ?--force-biarch ? ?attempt to build both architectures ? ? ? ? ? ? ? ? ? ? ? ?even if there is a non-empty configure.win ? ? ?--merge-multiarch bi-arch by merging from a tarball (from R-exts section 1.3.1 of a current R-devel it looks like this argument might be --force-multiarch)
--force-multiarch is an argument to R CMD check, unfortunately not R CMD INSTALL. As far as I know, for Mac (which I am guessing you are asking about) there is no R-centric way to do this; you could automate it with a script. Dan
Martin
Thanks, b
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