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

[Simon Urbanek]

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
>
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