install qvalue in R

Question

[yueli7]

Hi,

I try to install qvalue in R

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
A newer version of Bioconductor is available after installing a new version of
  R, ?BiocUpgrade for help
> biocLite("qvalue")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'qvalue'
试开URL'http://bioconductor.org/packages/2.13/bioc/src/contrib/qvalue_1.36.0.tar.gz'
Content type 'application/x-gzip' length 500738 bytes (489 Kb)
打开了URL
==================================================
downloaded 489 Kb

* installing *source* package 'qvalue' ...
** R
** data
** inst
** preparing package for lazy loading
警告: S3方法'as.character.tclObj', 'as.character.tclVar', 'as.double.tclObj', 'as.integer.tclObj', 'as.logical.tclObj', 'as.raw.tclObj', 'print.tclObj', '[[.tclArray', '[[<-.tclArray', '$.tclArray', '$<-.tclArray', 'names.tclArray', 'names<-.tclArray', 'length.tclArray', 'length<-.tclArray', 'tclObj.tclVar', 'tclObj<-.tclVar', 'tclvalue.default', 'tclvalue.tclObj', 'tclvalue.tclVar', 'tclvalue<-.default', 'tclvalue<-.tclVar', 'close.tkProgressBar'在NAMESPACE里有声明但不存在
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: 这个系统不支持Tcl/Tk
ERROR: lazy loading failed for package 'qvalue'
* removing '/home/li/R/x86_64-unknown-linux-gnu-library/3.0/qvalue'

The downloaded source packages are in
    '/tmp/RtmpaIchwR/downloaded_packages'
警告信息：
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package 'qvalue' had non-zero exit status

What can I do at this point?

Thanks!
Yue

[Giovanni M Dall'Olio]

Sorry but we can't read the error, it is in Chinese :-)

It seems that you have to install Tcl/TK on your system. Which operating system are you using?

Answer 1

[jake.hagen]

You need to install a package for your linux distribution. Look at this discussion

For example, from the link above

(3) Under Ubuntu Linux you can obtain the aforesaid development version by:

sudo apt-get install tcl8.5-dev tk8.5-dev

Also, according to this discussion you should install the development version of R to avoid these problems in the future.

[karl.stamm]

In my answer I said it can be difficult and you need sysadmin help, because not everyone has access to the command "sudo apt-get". This is the correct solution if the user is technically capable.

[yueli7]

sudo apt-get install tcl8.5-dev tk8.5-dev

and configure R

Thanks!

I appreciate!

Answer 2

[karl.stamm]

The qvalue package comes with a GUI tool, and so requires R to have been installed with the optional TCL/TK libraries.

I've seen this problem before and it's not easy to change your R. Maybe your Sysadmin can reinstall R with the TCL/TK libraries, but if you dont have those either, it can take some effort.

My solution was to download the sourcecode for qvalue, and remove those parts. the GUI is easy to delete and then qvalue can install cleanly.