[BioC] ReadAffy crashes R-devel on mac

[Helen Zhou]

--- Diego Diez <diez at kuicr.kyoto-u.ac.jp> 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.
> 
Dear Diego

Thanks for your advice, I will definitely keep that in
mind!! However, I'm afraid it doesn't solve my problem
- although it does slightly shift it. 

After reinstalling R-devel, fiddling around with a lot
of things, updating/installing packages from source, I
finally got Biobase working :). Only to get the
problem with affyio instead :(

> library(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)'.

> sessionInfo()
R version 2.7.0 Under development (unstable)
(2008-02-12 r44439) 
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] Biobase_1.17.13
> library(affyio)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library
'/Library/Frameworks/R.framework/Versions/2.7/Resources/library/affyio/libs/i386/affyio.so':
 
dlopen(/Library/Frameworks/R.framework/Versions/2.7/Resources/library/affyio/libs/i386/affyio.so,
6): Library not loaded: /usr/lib/libiconv.2.dylib
  Referenced from:
/Library/Frameworks/R.framework/Versions/2.7/Resources/library/affyio/libs/i386/affyio.so
  Reason: Incompatible library version: affyio.so
requires version 7.0.0 or later, but libiconv.2.dylib
provides version 5.0.0
Error: package/namespace load failed for 'affyio'

Will continue trying though; am still hopeful.

Best
- Helen

> 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")
> > > >
> > > >  *** caught bus error ***
> > > > address 0xc, cause 'non-existent physical
> address'
> > > >
> > > > Traceback:
> > > >  1: .Call("ReadHeader",
> > > as.character(filenames[[1]]),
> > > > PACKAGE = "affyio")
> > > >  2: read.affybatch(filenames = l$filenames,
> > > phenoData
> > > > = l$phenoData,     description =
> l$description,
> > > notes
> > > > = notes, compress = compress,     rm.mask =
> > > rm.mask,
> > > > rm.outliers = rm.outliers, rm.extra =
> rm.extra,
> > >
> > > > verbose = verbose, sd = sd, cdfname = cdfname)
> > > >  3: ReadAffy("GSM172068.CEL")
> > > >
> > > > Possible actions:
> > > > 1: abort (with core dump, if enabled)
> > > > 2: normal R exit
> > > > 3: exit R without saving workspace
> > > > 4: exit R saving workspace
> > > > Selection:
> > > >
> > > > Regards
> > > > - Helen
> > > >
> > > >
> > > >
> > >
> >
>
____________________________________________________________________________________
> > > > Be a better friend, newshound, and
> 
=== message truncated ===



      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page.