[BioC] [R-SIG-Mac] Trouble installing bioconductor packages on 64 bit R on OS X Leopard
Patrick Aboyoun
paboyoun at fhcrc.org
Thu Feb 14 00:34:28 CET 2008
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
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>>
>
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