error using biocLite: not found

Question

[lien]

Dear all,

I've just got a new computer, and would like to install R and several of the packages withing R, with the ultimate goal of running the cummeRbund package.

The operating system is Ubuntu 14.04 LTS. I installed R through the 'sudo apt-get install' command (R version 3.0.2 (2013-09-25) -- Frisbee Sailing.

When I try to use biocLite to install other packages, this doesn't work. It seems like nothing is going on, no error messages on the screen. When I wait long enough, it shows the error message: biocLite not found.

So far, I couldn't really find a way to install the biocLite separately, if that is even possible.

See the command below: the terminal gets blocked for like half an hour, than it says: unable to connect to bioconductor.

lien@lien:~$ sudo R
[sudo] password for lien:

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
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")
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  unable to connect to 'www.bioconductor.org' on port 80.
>

Alternatively, when I already ask for the biocLite, it says "could not find function "biocLite"".

lien@lien:~$ sudo R
[sudo] password for lien:

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
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")
biocLite('cummeRbund')
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  unable to connect to 'www.bioconductor.org' on port 80.
> biocLite('cummeRbund')
Error: could not find function "biocLite"
>

Not being an informatician, but really needing the R installation, all suggestions are welcome.

Thanks,
Lien

[Ram]

Why sudo R? Try just R

[lien]

I thought you needed sudo R if you wanted to install some packages?

[Ram]

Not really. Try without the sudo.

Answer 1

[matted]

Is the machine connected to the internet? I get the same error when I try to source biocLite with my internet turned off: "cannot open the connection."

[lien]

Yes, I do have internet connection.

Ok, when I open R without the sudo it's better: the biocLite is workiing. But still get some error: installation of package 'cummeRbund' had non-zero exit status.

> biocLite('cummeRbund')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'cummeRbund'
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/cummeRbund_2.4.1.tar.gz'
Content type 'application/x-gzip' length 2273444 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb*

** installing *source* package 'cummeRbund' ...
** R
** data
** inst
** preparing package for lazy loading
Error : object 'sqliteQuickSQL' is not exported by 'namespace:RSQLite'
Error : package 'Gviz' could not be loaded
ERROR: lazy loading failed for package 'cummeRbund'
* removing '/home/lien/R/x86_64-pc-linux-gnu-library/3.0/cummeRbund'*

*The downloaded source packages are in
    '/tmp/RtmpACwMdk/downloaded_packages'
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package 'cummeRbund' had non-zero exit status
2: installed directory not writable, cannot update packages 'AnnotationDbi',
  'Biobase', 'biovizBase', 'chron', 'colorspace', 'DBI', 'Formula',
  'GenomicFeatures', 'GenomicRanges', 'Hmisc', 'IRanges', 'labeling', 'plyr',
  'RColorBrewer', 'RCurl', 'rggobi', 'rgl', 'RGtk2', 'Rsamtools', 'RSQLite',
  'rtracklayer', 'scales', 'boot', 'class', 'cluster', 'codetools', 'foreign',
  'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart',
  'spatial'
>

When I try using the install.packages, it says that the package is not available.

> install.packages('cummeRbund', dependencies = TRUE)
Installing package into '/home/lien/R/x86_64-pc-linux-gnu-library/3.0'
(as 'lib' is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning message:
package 'cummeRbund' is not available (for R version 3.0.2)

[Devon Ryan]

install.packages() will never install Bioconductor packages. You must either download the package tar-ball or use biocLite() (I recommend the latter option, the former would be a real pain).

The error message is because something else (namely RSQLite) isn't installed correctly. Try removing and reinstalling it.