[BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)

Karl Brand k.brand at erasmusmc.nl
Thu Nov 24 15:51:41 CET 2011 

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")
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

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")
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'
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'
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")
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'
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'
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")
> 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 - 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>
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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