problems installing lumi
3
0
Entering edit mode
@hermann-norpois-5483
Last seen 8.3 years ago
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]]
lumi lumi • 1.7k views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 14 days ago
United States
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
ADD COMMENT
0
Entering edit mode
Pan Du ▴ 440
@pan-du-4636
Last seen 8.3 years ago
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 > ********************************************
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 2 hours ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 490 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6