Hi Mike, "sudo apt-get install libcurl4-openssl-dev" Solved the problem :) I now have: > library("DAVIDQuery") Loading required package: RCurl Loading required package: bitops This is DAVIDQuery Version 1.14.0 2010-06-10 > Many thanks! I'd still appreciate a tip on appropriate ways to add to R's PATH if and when the time comes (must be inevitable...) Karl On 2011-11-24 17:04, Mike Smith wrote: > Hi Karl, > > When I've encounted this problem with installing the RCurl package on > Ubuntu I've found that the following installed the appropriate libraries: > > apt-get install libcurl4-openssl-dev > > I didn't have to change R's path or anything like that. > > Hope it helps, > Mike > > On Thu, Nov 24, 2011 at 2:51 PM, Karl Brand <k.brand at="" erasmusmc.nl=""> <mailto:k.brand at="" erasmusmc.nl="">> wrote: > > Thank you Dan, James, Martin re. DAVIDQuery. > > Ok, install.packages() was NOT a good start, but a lesson i think > i'll remember thanks to the surprisingly restrained pointers :) > > But within either emacs/ess or a terminal running "sudo R --vanilla" > i fail to install "DAVIDQueary" using: > > source("http://www.__bioconductor.org/biocLite.R > <http: www.bioconductor.org="" bioclite.r="">") > biocLite("DAVIDQuery"). > > FWIW, the output from the emacs/ess session, and below that, from > the terminal (near identical) at the bottom of this message. > > To my inexperienced eye - this seems to be where the problems begin: > > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > > I found this with google: http://www.omegahat.org/RCurl/__FAQ.html > <http: www.omegahat.org="" rcurl="" faq.html=""> > > Which suggests that i verify the presence of libcurl on my system, > and if present, point R to it. 'locate libcurl' returns several > lines of locations and files, including: /usr/lib32/libcurl.so > > Now i'm guessing pointing R's "PATH" variable to /usr/lib32 will > solve my problems. What is the most appropriate way to do this? > Presently i have: > > > Sys.getenv("PATH") > [1] > "/usr/local/sbin:/usr/local/__bin:/usr/sbin:/usr/bin:/sbin:/__bi n:/usr/games" > > How do i add "/usr/lib32" to this? > > > help(Startup) > > Contains a lot of info that i don't feel experienced enough to act > on (without buggering up what is otherwise working). Would anyone > here at BioC care to share their thoughts on how to (persistently) > add to R's search path? This is probably what's needed to close this > thread, although i understand it may now be a Q for the general [R] > forum. > > With thanks in advance for further patient responders, > > Karl > > > > ################# ess/emacs output ##################### > > > .help.ESS <- help > > options(STERM='iESS', editor='emacsclient') > > source("http://www.__bioconductor.org/biocLite.R > <http: www.bioconductor.org="" bioclite.r="">") > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("DAVIDQuery") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'DAVIDQuery' > > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13? > (as ?lib? is unspecified) > also installing the dependency ?RCurl? > > trying URL 'http://cran.fhcrc.org/src/__contrib/RCurl_1.7-0.tar.gz > <http: cran.fhcrc.org="" src="" contrib="" rcurl_1.7-0.tar.gz="">' > Content type 'application/x-gzip' length 813252 bytes (794 Kb) > opened URL > ==============================__==================== > downloaded 794 Kb > > trying URL > 'http://www.bioconductor.org/__packages/2.9/bioc/src/contrib/__D AVIDQuery_1.14.0.tar.gz > <http: www.bioconductor.org="" packages="" 2.9="" bioc="" src="" contrib="" david="" query_1.14.0.tar.gz="">' > Content type 'application/x-gzip' length 186887 bytes (182 Kb) > opened URL > ==============================__==================== > downloaded 182 Kb > > * installing *source* package ?RCurl? ... > ** package ?RCurl? successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/kbrand/R/x86_64-pc-__linux-gnu- library/2.13/RCurl? > ERROR: dependency ?RCurl? is not available for package ?DAVIDQuery? > * removing > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13/__DAVIDQuery? > > The downloaded packages are in > ?/tmp/RtmpgNN770/downloaded___packages? > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?RCurl? had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?DAVIDQuery? had non-zero exit status > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > ######################### terminal output ################## > > kbrand at kbrand:~$ sudo R --vanilla > [sudo] password for kbrand: > > R version 2.14.0 (2011-10-31) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > source("http://www.__bioconductor.org/biocLite.R > <http: www.bioconductor.org="" bioclite.r="">") > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("DAVIDQuery") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'DAVIDQuery' > > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13? > (as ?lib? is unspecified) > also installing the dependency ?RCurl? > > trying URL 'http://cran.fhcrc.org/src/__contrib/RCurl_1.7-0.tar.gz > <http: cran.fhcrc.org="" src="" contrib="" rcurl_1.7-0.tar.gz="">' > Content type 'application/x-gzip' length 813252 bytes (794 Kb) > opened URL > ==============================__==================== > downloaded 794 Kb > > trying URL > 'http://www.bioconductor.org/__packages/2.9/bioc/src/contrib/__D AVIDQuery_1.14.0.tar.gz > <http: www.bioconductor.org="" packages="" 2.9="" bioc="" src="" contrib="" david="" query_1.14.0.tar.gz="">' > Content type 'application/x-gzip' length 186887 bytes (182 Kb) > opened URL > ==============================__==================== > downloaded 182 Kb > > * installing *source* package ?RCurl? ... > ** package ?RCurl? successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/kbrand/R/x86_64-pc-__linux-gnu- library/2.13/RCurl? > ERROR: dependency ?RCurl? is not available for package ?DAVIDQuery? > * removing > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13/__DAVIDQuery? > > The downloaded packages are in > ?/tmp/RtmpI5FdwF/downloaded___packages? > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?RCurl? had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?DAVIDQuery? had non-zero exit status > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > > > > > > > On 2011-11-23 18:39, Martin Morgan wrote: > > On 11/23/2011 08:34 AM, Karl Brand wrote: > > > Esteemed BioC UseRs and Devs, > > I'm trying (and failing) to install the BioC package > "DAVIDQuery". There > must be a simple way to solve this issue, but my googling > failed to > solve this issue. > > Within (ESS/Emacs) R --vanilla i tried: > > > install.packages("DAVIDQuery", dependencies=TRUE) > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13? > (as ?lib? is unspecified) > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?DAVIDQuery? is not available (for R version 2.14.0) > > > DAVIDQuery is a Bioconductor package, but it sounds like you're > choosing > a 'CRAN' archive. The recommended installation process is > > source("http://bioconductor.__org/biocLite.R > <http: bioconductor.org="" bioclite.r="">") > biocLite("DAVIDQuery") > > > > > > This makes me wonder if i need to specify a different > library (path). If > so, which one? > > > .libPaths() > [1] "/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13" > [2] "/usr/local/lib/R/site-__library" > [3] "/usr/lib/R/site-library" > [4] "/usr/lib/R/library" > > > That there are four is due to someone / thing other than R; see > ?Startup > for hints on how these libraries are identified. > > Martin > > > (This is a bigger area of ignorance for me - why has R set > up four > separate libraries by default? Where some require use of sudo to > install/update packages, whilst others do not? And what are the > implications when it comes time to upgrade to the next > version of R? I > have obtained some advice on this before - > https://stat.ethz.ch/__pipermail/ess- help/2011-__September/007120.html > <https: stat.ethz.ch="" pipermail="" ess-="" help="" 2011-september="" 007120.html=""> > - but > have failed to implement this given my focus on just using > R, neglecting > its proper maintenance, and all round inexperience with linux). > > I'd really appreciate responses on getting "DAVIDQuery" > running on my > currently installed R 2.14.0 (as well as any tips on 'good > practice' > when it comes to R library management on linux (ubuntu)). > > Sincerely, > > Karl > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.14.0 tools_2.14.0 > > > > > > > -- > Karl Brand <k.brand at="" erasmusmc.nl="" <mailto:k.brand="" at="" erasmusmc.nl="">> > Department of Genetics > Erasmus MC > Dr Molewaterplein 50 > 3015 GE Rotterdam > P +31 (0)10 704 3455 <tel:%2b31%20%280%2910%20704%203455> | F +31 > (0)10 704 4743 <tel:%2b31%20%280%2910%20704%204743> | M +31 (0)642 > 777 268 <tel:%2b31%20%280%29642%20777%20268> > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > -- > Mike Smith > PhD Student > Computational Biology Group > Cambridge University > -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268