[BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)
Karl Brand
k.brand at erasmusmc.nl
Thu Nov 24 18:15:50 CET 2011
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:/__bin:/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/__DAVIDQuery_1.14.0.tar.gz
> <http://www.bioconductor.org/packages/2.9/bioc/src/contrib/DAVIDQuery_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/__DAVIDQuery_1.14.0.tar.gz
> <http://www.bioconductor.org/packages/2.9/bioc/src/contrib/DAVIDQuery_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>
>
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>
>
>
>
> --
> 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
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