[R-SIG-Mac] Trouble installing bioconductor packages on 64 bit R on OS X Leopard

[Matthew Keller]

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