[BioC] Cannot load preprocessCore.so

[Martin Morgan]

Hi Peter

Peter Robinson <peter.robinson at t-online.de> writes:

> Hi conductors,
>
> I am trying to install Bioconductor on a new computer (debian linux)
> and just went through
>
> source("http://bioconductor.org/biocLite.R")
> biocLite()
>
> However, six packages had a nonzero exit status, and if I then enter
> "library(affy)", the system complains it cannot find preprocessCore.so
> (see below).
> Any ideas what is going wrong?

Probably there were error messages with biocLite that generated the
warnings, probably when the library preprocessCore was being
installed. Try

> biocLite('preprocessCore')

by itself.

> I could not find anything with google.

I visited http://bioconductor.org -> mailing lists -> search and
looked for preprocessCore.so, leading me to this helpful post from
Sean Davis

http://article.gmane.org/gmane.science.biology.informatics.conductor/17370

suggesting that your debian needs gfortran, which I think is obtained
with sudo apt-get install gfortran. If this does not help, it would be
helpful to see the output of biocLite('preprocessCore')

Martin

> thanks-peter
>
>
> The downloaded packages are in
>        /tmp/RtmpZuhaJ3/downloaded_packages
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  installation of package 'affy' had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  installation of package 'annaffy' had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  installation of package 'matchprobes' had non-zero exit status
> 4: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  installation of package 'vsn' had non-zero exit status
> 5: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  installation of package 'gcrma' had non-zero exit status
> 6: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  installation of package 'affyPLM' had non-zero exit status
>  > library(affy)
> Lade nötiges Paket: Biobase
> Lade nötiges Paket: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Lade nötiges Paket: affyio
> Lade nötiges Paket: preprocessCore
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  kann shared library
>  /usr/local/lib/R/site-library/preprocessCore/libs/preprocessCore.so'
>  nicht laden:
> libRlapack.so: Kann die Shared-Object-Datei nicht öffnen: Datei oder
> Verzeichnis nicht gefunden
> Fehler: Paket 'preprocessCore' konnte nicht geladen werden
>
> (translation: Could not load shared library preprocessCore)
>
>
>  > sessionInfo()
> R version 2.7.1 (2008-06-23)
> i486-pc-linux-gnu
>
> locale:
> LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE at euro;LC_COLLATE=de_DE at euro;LC_MONETARY=C;LC_MESSAGES=de_DE at euro;LC_PAPER=de_DE at euro;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE at euro;LC_IDENTIFICATION=C 
>
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] affyio_1.6.1  Biobase_2.0.1
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793