Thanks James, I tried (since I don't have root) source("http://www.bioconductor.org/biocLite.R") biocLite("GEOquery",lib = '/home/izg/R/x86_64-redhat-linux-gnu- library' ) it was failed by short of package RCurl, so I installed RCurl in '/home/izg/R/x86_64-redhat-linux-gnu-library' as well, then try again: biocLite("GEOquery", lib = '/home/izg/R/x86_64-redhat-linux-gnu- library' ) Running biocinstall version 2.3.13 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor. also installing the dependency 'RCurl' trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_0.98-1.tar.gz' Content type 'application/x-gzip' length 486610 bytes (475 Kb) opened URL ================================================== downloaded 475 Kb trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/GEOq uery_2.6.0.tar.gz' Content type 'application/x-gzip' length 136228 bytes (133 Kb) opened URL ================================================== downloaded 133 Kb * Installing *source* package 'RCurl' ... ... ... ... ... ** building package indices ... * DONE (RCurl) * Installing *source* package 'GEOquery' ... ** R ** inst ** preparing package for lazy loading Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RCurl Loading required package: bitops Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/izg/R/x86_64-redhat-linux-gnu- library/RCurl/libs/RCurl.so': libcurl.so.4: cannot open shared object file: No such file or directory Error: package 'RCurl' could not be loaded Execution halted ERROR: lazy loading failed for package 'GEOquery' ** Removing '/home/izg/R/x86_64-redhat-linux-gnu-library/GEOquery' The downloaded packages are in /tmp/Rtmphp1tUO/downloaded_packages Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'GEOquery' had non-zero exit status Then I goto '/home/izg/R/x86_64-redhat-linux-gnu-library/RCurl/libs/' and found there is nothing here, all library has been deleted somehow. even if I copy/install those lib again, it always happened like this. I tried to change the mode of this libraries as read-only, it's still been deleted anyhow. Thanks. Zhihua. ----- Original Message ---- From: James W. MacDonald <jmacdon@med.umich.edu> Cc: bioconductor at stat.math.ethz.ch Sent: Monday, August 3, 2009 12:30:40 PM Subject: Re: [BioC] GEOquery installation problem zhihua zhang wrote: > Hi, > I was trying to install GEOquery_1.7.2.tar.gz into my R (version 2.8.1 ). Because I am not root, so I did the following > >> install.packages("~/download/GEOquery_1.7.2.tar.gz", dependencies = TRUE, repos = NULL) > > This is what I got: > > Warning in install.packages("~/download/GEOquery_1.7.2.tar.gz", dependencies = TRUE, : > argument 'lib' is missing: using '/home/izg/R/x86_64-redhat-linux- gnu-library/2.8' > * Installing *source* package 'GEOquery' ... > ** R > ** inst > ** preparing package for lazy loading > Error in makeClassRepresentation(Class, properties, superClasses, prototype, : element 2 is empty; > the part of the args list of 'list' being evaluated was: > (header = list(), ) > Error: unable to load R code in package 'GEOquery' > Execution halted > ERROR: lazy loading failed for package 'GEOquery' > ** Removing '/home/izg/R/x86_64-redhat-linux-gnu- library/2.8/GEOquery' > Warning message: > In install.packages("~/download/GEOquery_1.7.2.tar.gz", dependencies = TRUE, : > installation of package '/home/izg/download/GEOquery_1.7.2.tar.gz' had non-zero exit status > > I searched in this mailist and found no answer, neither dose in google, > What am I gonna do then? I would recommend installing the package the correct way, as the version you seem to have downloaded is AFAIK not the correct version for your version of R. source("http://www.bioconductor.org/biocLite.R") biocLite("GEOquery") Pointing to a downloaded file and saying dependencies = TRUE, repos = NULL is not going to do what you seem to think it will. You can only get the correct dependencies if you point to a CRAN type repository, which is what biocLite() will do for you. Best, Jim > > Thanks > > Zhihua. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

I had a similar problem with GEOQuery and a missing libcurl as non- root user. What worked for me was: (1) install libcurl (not the R-package but the library) locally on your system. The __only__ version that provided the correct interfaces was "curl-7.16.4", all others failed (I tried 5 or so ...), especially those mentioned in the GEOQuery manual. The call should be sth like: ./configure --prefix=$HOME --enable-shared make && make install Be sure the curl-directory's lib-subdirectory contains libcurl.so, libcurl.so4 (and some more) afterwards (2) modify your ~/.bashrc (zshrc, whatever) by adding the lib to your path: export LD_LIBRARY_PATH=/path/to/curl/curl-7.16.4/lib/ (3) export PATH=$PATH:/path/to/curl/curl-7.16.4/bin (this step may be optional) (4) start R and use install.packages('RCurl', lib='$RH/library', repos='http://ftp5.gwdg.de/pub/misc/cran/') biocLite('GEOquery', lib='$RH/library') Works fine for me and should survive new installations since the libraries are found by now. Tobias zhihua zhang schrieb: > > > ----- Original Message ---- > From: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> > To: zhihua zhang <biozhang2001 at="" yahoo.com.cn=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Monday, August 3, 2009 5:25:04 PM > Subject: Re: [BioC] GEOquery installation problem > > >> ---Right, libcurl was not in my system, the third line command I was trying to install a local copy of libcurl as you said. >> > > Did that work? You just showed: > > ~/tmp/curl-7.19.5> make install > > Since you're not an admin, this couldn't have worked w/o choosing an appropriate prefix during the configure step -- what did you use? > -- yes, I made it into my home ~/local/ > > >> Are you saying that there is no RCurl folder at all in /home/izg/R/x86_64-redhat-linux-gnu-library, or that there is a folder, but there's nothing inside it? >> >> -- there is a folder call RCurl in /home/izg/R/x86_64-redhat-linux- gnu-library, just not any files in the folder however. >> > > Just out of curiosity -- in your previous emails, you showed some R commands to install RCurl, and then say that "all those seems successfully done!" And yet there is nothing in those directories ... did R not report an error during RCurl install? > > -- no, actually, before I try to load RCurl, it's alright. The Rcurl installation didn't report any error. > > > install.packages("RCurl",lib = '/home/izg/R/x86_64-redhat-linux-gnu- library') > it says > ... > ** building package indices > * DONE (RCurl) > > The downloaded packages are in > /tmp/RtmpYm80DR/downloaded_packages > > but there is nothing in the folder :~/R/x86_64-redhat-linux-gnu- library/RCurl/libs > and I can not load > > >> library("RCurl", lib.loc="/home/izg/R/x86_64-redhat-linux-gnu- library/") >> > Error in library("RCurl", lib.loc = "/home/izg/R/x86_64-redhat- linux-gnu-library/") : > no library trees found in 'lib.loc' > > > > >> -- do you mean to modify the Makefile of RCurl to link to the locally installed libcurl? >> > > No, I don't think you have to modify any Makefiles, but you'll need to tell R where to find your installed libcurl. > > When calling install.packages, I believe you can pass this info in through the "configure.args" parameter. I'M JUST GUESSING, but maybe something like this would work: > > install.packages("RCurl", configure.args=c(RCurl='-I/home/izg/local/include -L/home/izg/local/lib -lcurl')) > > First thing is first, though, and you have to make sure that libcurl is installed correctly, and also know what --prefix you used when configuring/installing it. > > -- I tried, system even said > > configure: error: unrecognized option: -I/home/izhang/local/include/ > Try `./configure --help' for more information. > ERROR: configuration failed for package 'RCurl' > > Thanks. > > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > 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 > > -- =============================================================== Tobias Petri =============================================================== LFE Bioinformatik Amalienstr. 17 80333 M?nchen, DE =============================================================== mail : tobias.petri at bio.ifi.lmu.de phone : +49 89 2180 4042 web : http://www.bio.ifi.lmu.de/mitarbeiter/tobias-petri ===============================================================