[BioC] Trouble installing bioconductor packages on 64 bit R on OS X Leopard

Matthew,
As Simon pointed out, the affyio package was probably already installed
on your machine without x86_64 architecture support, so when you tried
to build affy, which depends on affyio, from source on the x86_64
architecture you got an error. Here are two suggestions for addressing
this issue:

1) Rebuild affyio from source under the x86_64 architecture.

2) Use the universal BioC 2.2 binary packages (i386, x86_64, ppc)
produced by the Bioconductor core team.
    [Note:  R 2.6.x and the associated pre-built BioC 2.1 universal Mac
OS X binaries only support the i386 and ppc architectures]

    Steps:
    a) Upgrade from R 2.6.2 alpha (2008-01-29 r44238) to R-devel
(required for BioC 2.2)
    You can grab
http://r.research.att.com/R-devel-leopard-universal.tar.gz to make your
life easier.

    b) Use biocLite() to download and install the universal Mac OS X
binary packages.


Cheers,
Patrick




Simon Urbanek wrote:

Matthew,

it's hard to tell without seeing what *is* actually installed, but my
guess would be that some packages (e.g. affyio ?) are only partially
installed (maybe from previous attempts). The automatic dependency
resolution looks only whether the dependencies are present, not
whether they work. Therefore make sure you install those incomplete
dependencies first.

As an aid, you can use something like this:
for i in `ls -d */libs`; do if [ ! -e $i/x86_64 ]; then echo $i; fi;
done
in your library directory to see which packages have missing libs for
x86_64.

Also note that if a package has a configure script, you have to
install it manually for each architecture, because the sources have to
be newly unpacked for each run (see the FAQ).

Finally, I thought that BioC folks are building 64-bit binaries, so
you should not need to go through all this - but I may be wrong - try
asking them.

Cheers,
Simon



On Feb 13, 2008, at 5:20 PM, Matthew Keller wrote:

Hello all,

I've been working on this for hours. Have gone through the FAQs,
Simon's R for Mac OS X Developer's Page, and various threads on the
listserves. I.e., I feel like I've followed all the instructions I can
find, yet to no avail.

On newest intel MacPro with Leopard, I have 64 bit R installed finally
(figuring out that I did not have gcc-4.2, then getting it, and then
figuring out how to add the PATH variables was not trivial). However,
I cannot install bioconductor nor any of the bioconductor packages. As
suggested on a previous response, I have set
options(pkgType="source"). But when R tries to install dependency
libraries, it is saying, eg, that " 'affyio' is not installed for
'arch=x86_64" etc.  I thought by saying pkgType="source" I WAS having
R install the 64 bit libraries, including dependencies, from source.
Do I need to erase all existing libraries, or are the 64 bit libraries
somewhere different and I need to tell R where they are, or what? At
this point I'm grasping for straws, so before I start doing things at
random, I was hoping I could get some help.

Below I'll give specifics, but any help would be most appreciated!

At the end of my rope...

Matt

sessionInfo()

R version 2.6.2 alpha (2008-01-29 r44238)
i386-apple-darwin9.1.0

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] MASS_7.2-40 boot_1.2-30 tools_2.6.2

.Machine$sizeof.pointer

[1] 8


I then do the following:

source("http://bioconductor.org/biocLite.R")

Warning messages:
1: In safeSource() : Redefining 'biocinstall'
2: In safeSource() : Redefining 'biocinstallPkgGroups'
3: In safeSource() : Redefining 'biocinstallRepos'

biocLite()

I then get hundreds of lines of output, but error messages within
them. And here is a small snippet of the errors I'm getting:


* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-DHAVE_ZLIB=1  -I/usr/local/include
-I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/
include"
 -fPIC  -g -O2 -c chipbackground.c -o chipbackground.o
i686-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
gcc-4.2 -arch x86_64 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-DHAVE_ZLIB=1  -I/usr/local/include
-I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/
include"
 -fPIC  -g -O2 -c getall_locations.c -o getall_locations.o
i686-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
gcc-4.2 -arch x86_64 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-DHAVE_ZLIB=1  -I/usr/local/include
-I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/
include"
 -fPIC  -g -O2 -c mas5calls.c -o mas5calls.o
i686-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
gcc-4.2 -arch x86_64 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-DHAVE_ZLIB=1  -I/usr/local/include
-I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/
include"
 -fPIC  -g -O2 -c rma2.c -o rma2.o
i686-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
gcc-4.2 -arch x86_64 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-DHAVE_ZLIB=1  -I/usr/local/include
-I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/
include"
 -fPIC  -g -O2 -c rma_background2.c -o rma_background2.o
i686-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
gcc-4.2 -arch x86_64 -std=gnu99 -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-DHAVE_ZLIB=1  -I/usr/local/include
-I"/Library/Frameworks/R.framework/Resources/library/preprocessCore/
include"
 -fPIC  -g -O2 -c rma_common.c -o rma_common.o
i686-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
-Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o affy.so chipbackground.o getall_locations.o
mas5calls.o rma2.o rma_background2.o rma_common.o -lz
-F/Library/Frameworks/R.framework/.. -framework R
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

 Vignettes contain introductory material. To view, type
 'openVignette()'. To cite Bioconductor, see
 'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Error: package 'affyio' is not installed for 'arch=x86_64'
Execution halted
ERROR: lazy loading failed for package 'affy'
** Removing '/Library/Frameworks/R.framework/Resources/library/affy'


--
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com