[BioC] [R-SIG-Mac] 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
More information about the Bioconductor
mailing list