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@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@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@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
>
> ______________________________**_________________
> Bioconductor mailing list
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> 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

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