Dear list, I had and still have trouble installing lumi. After an R update and the installation of the hdrcde package it still does not work with the lumi package via biocLite("lumi"). This is the answer (R version 2.15): And I was not able to install the packages with dependencies neither. I would be happy for some help. Thanks Hermann Norpois * installing *source* package ‘XML’ ... ** Paket ‘XML’ erfolgreich entpackt und MD5 Summen überprüft checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E No ability to remove finalizers on externalptr objects in this verison of R checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/usr/local/lib/R/site-library/XML’ * installing *source* package ‘RCurl’ ... ** Paket ‘RCurl’ erfolgreich entpackt und MD5 Summen überprüft checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’ * removing ‘/usr/local/lib/R/site-library/RCurl’ ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’ * removing ‘/usr/local/lib/R/site-library/rtracklayer’ ERROR: dependency ‘XML’ is not available for package ‘annotate’ * removing ‘/usr/local/lib/R/site-library/annotate’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’ * removing ‘/usr/local/lib/R/site-library/genefilter’ ERROR: dependencies ‘annotate’, ‘genefilter’ are not available for package ‘methylumi’ * removing ‘/usr/local/lib/R/site-library/methylumi’ ERROR: dependencies ‘methylumi’, ‘rtracklayer’, ‘annotate’ are not available for package ‘lumi’ * removing ‘/usr/local/lib/R/site-library/lumi’ [[alternative HTML version deleted]]

Hi Hermann -- nice to see you here. On 09/06/2012 01:02 AM, Hermann Norpois wrote: > Dear list, > > I had and still have trouble installing lumi. After an R update and the > installation of the hdrcde package it still does not work with the lumi > package via biocLite("lumi"). This is the answer (R version 2.15): And I > was not able to install the packages with dependencies neither. > > I would be happy for some help. > Thanks > Hermann Norpois > > * installing *source* package ?XML? ... > ** Paket ?XML? erfolgreich entpackt und MD5 Summen ?berpr?ft > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > No ability to remove finalizers on externalptr objects in this verison of R > checking for sed... /bin/sed > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config > ERROR: configuration failed for package ?XML? XML on non-Windows requires that the system XML library needs to be available. Likely you need to use your package manager to install libxml2-devel; for me on Ubuntu I would say sudo apt-get install libxml2-dev > * removing ?/usr/local/lib/R/site-library/XML? > * installing *source* package ?RCurl? ... > ** Paket ?RCurl? erfolgreich entpackt und MD5 Summen ?berpr?ft > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? curl is also a system dependency, sudo apt-get install libcurl3-dbg > * removing ?/usr/local/lib/R/site-library/RCurl? > ERROR: dependencies ?XML?, ?RCurl? are not available for package > ?rtracklayer? the rest of the errors look like they will be corrected by libxml and libcurl installation. Martin > * removing ?/usr/local/lib/R/site-library/rtracklayer? > ERROR: dependency ?XML? is not available for package ?annotate? > * removing ?/usr/local/lib/R/site-library/annotate? > ERROR: dependency ?annotate? is not available for package ?genefilter? > * removing ?/usr/local/lib/R/site-library/genefilter? > ERROR: dependencies ?annotate?, ?genefilter? are not available for package > ?methylumi? > * removing ?/usr/local/lib/R/site-library/methylumi? > ERROR: dependencies ?methylumi?, ?rtracklayer?, ?annotate? are not > available for package ?lumi? > * removing ?/usr/local/lib/R/site-library/lumi? > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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

Hi Hermann Based on your screen printout, I believe your R installation has problem. After R installation, try biocLite first. source('http://bioconductor.org/biocLite.R') biocLite() Then install R biocLite('lumi') If some required package cannot be installed. Try to install them manually. For example: install.package('hdrcde') Or you can download from CRAN website and install locally. After install missing dependent packages, try biocLite('lumi') again. Pan On Thu, Sep 6, 2012 at 3:00 AM, <bioconductor-request at="" r-project.org=""> wrote: > ------------------------------ > Date: Thu, 6 Sep 2012 10:02:14 +0200 > From: Hermann Norpois <hnorpois at="" googlemail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] problems installing lumi > Message-ID: > <cakyzebtm+yskj12eychfn=7chphxwjo_tduvzkijswexyn_z1w at="" mail.gmail.com=""> > Content-Type: text/plain > > Dear list, > > I had and still have trouble installing lumi. After an R update and the > installation of the hdrcde package it still does not work with the lumi > package via biocLite("lumi"). This is the answer (R version 2.15): And I > was not able to install the packages with dependencies neither. > > I would be happy for some help. > Thanks > Hermann Norpois > > * installing *source* package ?XML? ... > ** Paket ?XML? erfolgreich entpackt und MD5 Summen ?berpr?ft > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > No ability to remove finalizers on externalptr objects in this verison of R > checking for sed... /bin/sed > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config > ERROR: configuration failed for package ?XML? > * removing ?/usr/local/lib/R/site-library/XML? > * installing *source* package ?RCurl? ... > ** Paket ?RCurl? erfolgreich entpackt und MD5 Summen ?berpr?ft > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/usr/local/lib/R/site-library/RCurl? > ERROR: dependencies ?XML?, ?RCurl? are not available for package > ?rtracklayer? > * removing ?/usr/local/lib/R/site-library/rtracklayer? > ERROR: dependency ?XML? is not available for package ?annotate? > * removing ?/usr/local/lib/R/site-library/annotate? > ERROR: dependency ?annotate? is not available for package ?genefilter? > * removing ?/usr/local/lib/R/site-library/genefilter? > ERROR: dependencies ?annotate?, ?genefilter? are not available for package > ?methylumi? > * removing ?/usr/local/lib/R/site-library/methylumi? > ERROR: dependencies ?methylumi?, ?rtracklayer?, ?annotate? are not > available for package ?lumi? > * removing ?/usr/local/lib/R/site-library/lumi? > > [[alternative HTML version deleted]] > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 115, Issue 6 > ********************************************

Hi Hermann, On 9/6/2012 4:02 AM, Hermann Norpois wrote: > Dear list, > > I had and still have trouble installing lumi. After an R update and the > installation of the hdrcde package it still does not work with the lumi > package via biocLite("lumi"). This is the answer (R version 2.15): And I > was not able to install the packages with dependencies neither. > > I would be happy for some help. > Thanks > Hermann Norpois > > * installing *source* package ?XML? ... > ** Paket ?XML? erfolgreich entpackt und MD5 Summen ?berpr?ft > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > No ability to remove finalizers on externalptr objects in this verison of R > checking for sed... /bin/sed > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config Big hint here ^^^^^^^^^^^^^^^ You need libxml2 and libxml2-devel. Best, Jim > ERROR: configuration failed for package ?XML? > * removing ?/usr/local/lib/R/site-library/XML? > * installing *source* package ?RCurl? ... > ** Paket ?RCurl? erfolgreich entpackt und MD5 Summen ?berpr?ft > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/usr/local/lib/R/site-library/RCurl? > ERROR: dependencies ?XML?, ?RCurl? are not available for package > ?rtracklayer? > * removing ?/usr/local/lib/R/site-library/rtracklayer? > ERROR: dependency ?XML? is not available for package ?annotate? > * removing ?/usr/local/lib/R/site-library/annotate? > ERROR: dependency ?annotate? is not available for package ?genefilter? > * removing ?/usr/local/lib/R/site-library/genefilter? > ERROR: dependencies ?annotate?, ?genefilter? are not available for package > ?methylumi? > * removing ?/usr/local/lib/R/site-library/methylumi? > ERROR: dependencies ?methylumi?, ?rtracklayer?, ?annotate? are not > available for package ?lumi? > * removing ?/usr/local/lib/R/site-library/lumi? > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099