To whom it may concern. As I would like to analyse some array data I was keen on downloading the lumi package that depends obviously on hdrcde that is not available for r 2.12.1. I did not find instructions to solve or circumvent this problem. Installing hdrcde by hand did not work either. It was not detected by> (.packages(all.available=TRUE))if installed in the R library. Thanks Hermann Norpois This was my try to install the lumi package:> source ("http://bioconductur.org/biocLite.R")Fehler in file(filenaReme, "r", encoding = encoding) : kann Verbindung nicht öffnen Zusätzlich: Warnmeldung: In file(filename, "r", encoding = encoding) : kann 'bioconductur.org' nicht auflösen> source ("http://bioconductor.org/biocLite.R")BiocInstaller version 1.2.1, ?biocLite for help> biocLite("lumi")BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'lumi' Installing package(s) into ‘/home/hnorpois/R/i686-pc- linux-gnu-library/2.14’ (as ‘lib’ is unspecified) Warnung: dependency ‘hdrcde’ is not available versuche URL ' http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz' Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb) URL geöffnet =================================================downloaded 10.9 Mb ERROR: dependency ‘hdrcde’ is not available for package ‘lumi’ * removing ‘/home/hnorpois/R/i686-pc-linux-gnu-library/2.14/lumi’ The downloaded packages are in ‘/tmp/RtmpMNrvTz/downloaded_packages’ Warnmeldungen: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ‘lumi’ had non-zero exit status 2: 'rgl' cannot be updated, installed directory '/usr/lib/R/site-library' not writeable [[alternative HTML version deleted]]
On 05.09.2012 11:41, Hermann Norpois wrote:> To whom it may concern. > > As I would like to analyse some array data I was keen on downloading the > lumi package that depends obviously on hdrcde that is not available for r > 2.12.1. I did not find instructions to solve or circumvent this problem. > Installing hdrcde by hand did not work either. It was not detected by >> (.packages(all.available=TRUE)) > if installed in the R library. > > Thanks > Hermann Norpois > > This was my try to install the lumi package: > >> source ("http://bioconductur.org/biocLite.R")This can easily be solved by using the correct spelling for "bioconductor". Uwe Ligges> Fehler in file(filenaReme, "r", encoding = encoding) : > kann Verbindung nicht ?ffnen > Zus?tzlich: Warnmeldung: > In file(filename, "r", encoding = encoding) : > kann 'bioconductur.org' nicht aufl?sen >> source ("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help >> biocLite("lumi") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'lumi' > Installing package(s) into ?/home/hnorpois/R/i686-pc- > linux-gnu-library/2.14? > (as ?lib? is unspecified) > Warnung: dependency ?hdrcde? is not available > versuche URL ' > http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz' > Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb) > URL ge?ffnet > =================================================> downloaded 10.9 Mb > > ERROR: dependency ?hdrcde? is not available for package ?lumi? > * removing ?/home/hnorpois/R/i686-pc-linux-gnu-library/2.14/lumi? > > The downloaded packages are in > ?/tmp/RtmpMNrvTz/downloaded_packages? > Warnmeldungen: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?lumi? had non-zero exit status > 2: 'rgl' cannot be updated, installed directory '/usr/lib/R/site-library' > not > writeable > > [[alternative HTML version deleted]] > > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
On 09/05/2012 02:41 AM, Hermann Norpois wrote:> To whom it may concern. > > As I would like to analyse some array data I was keen on downloading the > lumi package that depends obviously on hdrcde that is not available for r > 2.12.1. I did not find instructions to solve or circumvent this problem. > Installing hdrcde by hand did not work either. It was not detected by >> (.packages(all.available=TRUE)) > if installed in the R library. > > Thanks > Hermann Norpois > > This was my try to install the lumi package: > >> source ("http://bioconductur.org/biocLite.R") > Fehler in file(filenaReme, "r", encoding = encoding) : > kann Verbindung nicht ?ffnen > Zus?tzlich: Warnmeldung: > In file(filename, "r", encoding = encoding) : > kann 'bioconductur.org' nicht aufl?sen >> source ("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help >> biocLite("lumi") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'lumi' > Installing package(s) into ?/home/hnorpois/R/i686-pc- > linux-gnu-library/2.14? > (as ?lib? is unspecified) > Warnung: dependency ?hdrcde? is not available > versuche URL ' > http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz' > Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb) > URL ge?ffnet > =================================================> downloaded 10.9 Mb > > ERROR: dependency ?hdrcde? is not available for package ?lumi? > * removing ?/home/hnorpois/R/i686-pc-linux-gnu-library/2.14/lumi?If I use R-2.14 and install.packages("hdrcde", repos="http://cran.fhcrc.org") I get In getDependencies(pkgs, dependencies, available, lib) : package 'hdrcde' is not available (for R version 2.14.0 alpha) but if I use R-2.15 the package installs correctly. Likewise with biocLite("lumi"). So I think the easiest solution is to use a current version of R. Please ask questions about Bioconductor packages on the Bioconductor mailing list http://bioconductor.org/help/mailing-list/ Martin> > The downloaded packages are in > ?/tmp/RtmpMNrvTz/downloaded_packages? > Warnmeldungen: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?lumi? had non-zero exit status > 2: 'rgl' cannot be updated, installed directory '/usr/lib/R/site-library' > not > writeable > > [[alternative HTML version deleted]] > > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793