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

Hi Patrick, Simon, and everyone else,

 Thanks for the help. This was tougher than it should have been, but
 it's clearer to me now why I ran into this problem. I'll try to
 summarize in case others get into this jam. Here's what I did, then
 how I fixed it:

 1) downloaded R 64 bit
 2) installed the x code developer tools from my *new* Leopard disk
 (shipped with mac Jan 2008), which I understood to include gcc4-2
 3) installed gfortran-4.2.1
 4) start 64 bit R
 5) change options: options(pkgType="source")
 6) source("http://bioconductor.org/biocLite.R")
 7) biocLite()

 So it should work, right? Wrong. The problem is that I didn't have
 gcc4-2 installed, which the output told me about 100 times. So then:
 1) find and install gcc4-2
 2) redo the above

 So this should work right? Wrong. Now the R output tells me  that
 library X (e.g., affyio) "is not installed for 'arch=x86_64"  about 20
 times.

 In retrospect, the reason this happened is because some of the
 packages had either been installed by me before on 32 bit system, or
 they were only partially installed when I tried to install
 bioconductor without gcc4-2 (I can't remember which).

 What I did that works:
 1) remove ALL packages in anyway related to bioconductor by throwing
 them in the trash.
 2) redoing the above

 Now all is working. What SHOULD I have done? I should have done #2
 that Patrick recommended above.

 Best,

 Matt



 On Feb 13, 2008 4:34 PM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:

 > 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
 > >>
 > >>
 > >>

 > >
 > > _______________________________________________
 > > Bioconductor mailing list
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 > > https://stat.ethz.ch/mailman/listinfo/bioconductor
 > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
 > >

 >
 >

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