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

Max Kuhn mxkuhn at gmail.com
Thu Feb 14 18:55:40 CET 2008


I'm not sure what you should have done, but here is what I do:

Leave your regular library path alone (i.e. leave all of the 32 biy
package installs there).

Create a new path for 64 bit installs. I use

   /Library/Frameworks/R.framework/Versions/2.6/Resources/RLib64

Install all packages doing something like:

biocLite(
   c("annaffy", "annotate"),
   type = "source",
   lib = "/Library/Frameworks/R.framework/Versions/2.6/Resources/RLib64")

or

install.packages(
   pkgs = "geepack",
   type = "source",
   lib = "/Library/Frameworks/R.framework/Versions/2.6/Resources/RLib64")

Now, when you load R, you can use

if(.Machine$sizeof.pointer == 8)
   .libPaths("/Library/Frameworks/R.framework/Versions/2.6/Resources/RLib64")

There might be a cleaner way to accomplish the same thing.

Max


On Wed, Feb 13, 2008 at 7:02 PM, Matthew Keller <mckellercran at gmail.com> wrote:
> 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
>  > > Bioconductor at stat.math.ethz.ch
>  > > 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
>
>  _______________________________________________
>
>
> Bioconductor mailing list
>  Bioconductor at stat.math.ethz.ch
>  https://stat.ethz.ch/mailman/listinfo/bioconductor
>  Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 

Max



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