Question: install qvalue in R
0
gravatar for yueli7
2.4 years ago by
yueli710
China
yueli710 wrote:

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

 

qvalue • 2.0k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by yueli710

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?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Giovanni M Dall'Olio25k
1
gravatar for jake.hagen
2.4 years ago by
jake.hagen40
United States
jake.hagen40 wrote:

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

http://r.789695.n4.nabble.com/Where-is-the-tcltk-package-td3434915.html

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.

ADD COMMENTlink written 2.4 years ago by jake.hagen40

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.

ADD REPLYlink written 2.4 years ago by karl.stamm3.2k
0
gravatar for karl.stamm
2.4 years ago by
karl.stamm3.2k
United States
karl.stamm3.2k wrote:

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.

ADD COMMENTlink written 2.4 years ago by karl.stamm3.2k
0
gravatar for yueli7
2.4 years ago by
yueli710
China
yueli710 wrote:

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

and configure R

 

Thanks!

 

I appreciate!

ADD COMMENTlink written 2.4 years ago by yueli710
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1424 users visited in the last hour