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? I could not find anything with google. 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 n?tiges Paket: Biobase Lade n?tiges 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 n?tiges Paket: affyio Lade n?tiges 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 ?ffnen: 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

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/1 7370 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 n?tiges Paket: Biobase > Lade n?tiges 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 n?tiges Paket: affyio > Lade n?tiges 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 ?ffnen: 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 > > _______________________________________________ > 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 -- 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