[BioC] ReadAffy crashes R-devel on mac

[Helen Zhou]

--- Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
wrote:

> I would suggest installing from scratch, making sure
> that you install  
> from source and that your toolchain is set properly
> to compile from  
> scratch on the Mac. Most likely there is some
> mismatch between  
> compiler versions. 

Dear Kasper

Thanks for your reply - although this is probably
where I have to admit that I'm slightly lazy and
usually don't install from source but just form the
installer image (.dmg) at
http://r.research.att.com/... Guess I'll have to give
the installation from source a go at some point soon.

> If you want more information,
> tell us
>    1) Are you using Leopard?

No, Tiger 10.4.11

>    2) Exactly what compiler you are using (include
> the build number  
> please) and how did you install it.

Good question, it has been a while (for my last
computer update I just copied everything from my old
one with a firewire cable).
- I have Xcode 2.4.1., which I can't remember anything
about really.
- For fortran I have the GNU Fortran compiler from
http://r.research.att.com/tools/ installed when I did
the R-update and just run again today, i.e. version
4.2.1. Changed the path as indicated in the
instructions.

Best
- Helen

> The answer to 2) might be simple like "I never
> installed a compiler"  
> or "I installed Xcode 3 from the leopard disc" or
> ...
> 
> A good idea would be to read
> http://r.research.att.com/tools/
> carefully
> 
> Kasper
> 
> 
> 
> On Feb 13, 2008, at 7:42 AM, Diego Diez wrote:
> 
> > Hi Helen,
> >
> > (sorry for the double message I forgot to cc bioc)
> >
> > I found the same problem when installing BioC
> development packages
> > with R-devel in a PPC Mac. The reason might be
> that the binary
> > packages are not compiled for PPC in the devel
> branch although I am
> > not sure about it. Anyway, to solve it you should
> use source packages,
> > i.e. either:
> >
> > source('http://bioconductor.org/bioLite.R')
> > biocLite(type="source")
> >
> > or if you want to update your installation:
> >
> > library(Biobase)
> > update.packages(repos=biocReposList(),
> type="source")
> >
> > unfortunately, after realizing my problem I was
> unable to fix the
> > installation and I had to reinstall R-devel and
> BioC again. Maybe I
> > didn't too hard.
> >
> > Hope this helps.
> >
> > Diego.
> >
> > On Feb 13, 2008 8:06 PM, Helen Zhou
> <zhou.helen at yahoo.com> wrote:
> >> Dear Ben,
> >>
> >> thanks your for your fast reply. I actually
> thought I
> >> installed everything with biocLite() when I
> changed to
> >> R-devel a couple of weeks ago, but I guess I must
> have
> >> messed up somewhere.
> >>
> >> Unfortunately, I suspect that I have some issues
> with
> >> my installation. I updated the packages by
> running
> >>
> >>> repos <- biocReposList()
> >>> update.packages(repos=repos, ask=FALSE)
> >>
> >> but now, what ever I try I run into a problem
> with
> >> Biobase. My previous version was 1.17.8, but
> after the
> >> update it's 1.17.12, but I can't actually load
> it. In
> >> a new R-session with nothing else loaded:
> >>
> >>> library(Biobase)
> >> Loading required package: tools
> >> Error in dyn.load(file, ...) :
> >>   unable to load shared library
> >>
>
'/Library/Frameworks/R.framework/Versions/2.7/Resources/library/
> 
> >> Biobase/libs/i386/Biobase.so':
> >>
> >>
>
dlopen(/Library/Frameworks/R.framework/Versions/2.7/Resources/
> 
> >> library/Biobase/libs/i386/Biobase.so,
> >> 6): Library not loaded: /usr/lib/libiconv.2.dylib
> >>   Referenced from:
> >>
>
/Library/Frameworks/R.framework/Versions/2.7/Resources/library/
> 
> >> Biobase/libs/i386/Biobase.so
> >>   Reason: Incompatible library version:
> Biobase.so
> >> requires version 7.0.0 or later, but
> libiconv.2.dylib
> >> provides version 5.0.0
> >> Error: package/namespace load failed for
> 'Biobase'
> >>
> >> Regards
> >> - Helen
> >>
> >>
> >> --- Ben Bolstad <bmb at bmbolstad.com> wrote:
> >>
> >>> Looking at your sessionInfo() almost certainly
> your
> >>> affyio is out of
> >>> date (both for R-2.6.1 and R-2.7.0),
> >>>
> >>> Current Release version: 1.6.1
> >>> Current Devel version: 1.7.11
> >>>
> >>> Your error is likely due to mismatched versions
> of
> >>> the packages.
> >>>
> >>> Best,
> >>>
> >>> Ben
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Wed, 2008-02-13 at 02:07 -0800, Helen Zhou
> wrote:
> >>>> Dear list,
> >>>>
> >>>> oddly enough, whenever I try to read in
> affymetrix
> >>>> files my R-session crashes. This includes when
> I
> >>> try
> >>>> to re-run old scripts. I've never had this
> issue
> >>>> before, but updated from 2.6.1 to 2.7.0
> recently.
> >>>>
> >>>> Any help/comments would be much appreciated!
> The
> >>> full
> >>>> list of commands + sessionInfo is shown below.
> >>> I've
> >>>> tried with other cel files as well (affy mouse
> >>>> arrays), but the result is always the same.
> >>>>
> >>>>> setwd("~/Desktop")
> >>>>> library(affy)
> >>>> 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
> >>>> Loading required package: preprocessCore
> >>>>> sessionInfo()
> >>>> R version 2.7.0 Under development (unstable)
> >>>> (2007-12-22 r43762)
> >>>> i386-apple-darwin8.10.1
> >>>>
> >>>> locale:
> >>>>
> >>>
> >>
>
en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> >>>>
> >>>> attached base packages:
> >>>> [1] tools     stats     graphics  grDevices
> utils
> >>>
> >>>> datasets  methods   base
> >>>>
> >>>> other attached packages:
> >>>> [1] affy_1.17.3          preprocessCore_1.1.5
> >>>> affyio_1.5.11        Biobase_1.17.8
> >>>>> raw <- ReadAffy("GSM172068.CEL")
> >>>>
> 
=== message truncated ===



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