[BioC] Problem installing packages on new R

v.leoncikas at surrey.ac.uk v.leoncikas at surrey.ac.uk
Wed Feb 13 11:20:56 CET 2013


Dear Sir/Madam, 

I am writing to report the problem with installing certain packages in the new version on R. 
versions I am using iare:
    R version 2.15.2 (2012-10-26) 
    Bioconductor version 2.11 (BiocInstaller 1.8.3)

I was having difficulties in installing packages arrayMvout, lumi and XML and few others. However, nio probmlems when I tried install other packages like beadarray, i have experienced no problems.
To fix the problem I was reading lots of forums, but nothing worked. I went extreme, by removing R, bioconfuctor and any software from my computer related to R. After doing this,
R and Bioconductor were installed again. I tried to install beadarray and limma - both packages were installed without problems, but arrayMvout and lumi showed error. 

I have tried to install arrayMvout on the older version of R - no problem, it seems the new version is having some issues. 
Could you perhaps look into this problem? 

Thank you in advance, 

Kind regards,


Vytautas Leoncikas

Mr Vytautas Leoncikas
Postgraduate Researcher
Faculty of Health and Medical Science
Department of Biochemistry and Physiology
University of Surrey
GU2 7XH

P.s. Sending R output after trieing to install arrayMvout
>source("http://bioconductor.org/biocLite.R")
>biocLite("arrayMvout") 
 

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'arrayMvout'
also installing the dependencies ‘rgl’, ‘XML’, ‘ks’, ‘methylumi’, ‘annotate’, ‘hdrcde’, ‘genefilter’, ‘lumi’, ‘simpleaffy’

trying URL 'http://cran.fhcrc.org/src/contrib/rgl_0.93.928.tar.gz'
Content type 'application/x-gzip' length 1732458 bytes (1.7 Mb)
opened URL
==================================================
downloaded 1.7 Mb

trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.95-0.1.tar.gz'
Content type 'application/x-gzip' length 1724282 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

trying URL 'http://cran.fhcrc.org/src/contrib/ks_1.8.11.tar.gz'
Content type 'application/x-gzip' length 338410 bytes (330 Kb)
opened URL
==================================================
downloaded 330 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/methylumi_2.4.0.tar.gz'
Content type 'application/x-gzip' length 3590288 bytes (3.4 Mb)
opened URL
==================================================
downloaded 3.4 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/annotate_1.36.0.tar.gz'
Content type 'application/x-gzip' length 1868464 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb

trying URL 'http://cran.fhcrc.org/src/contrib/hdrcde_2.16.tar.gz'
Content type 'application/x-gzip' length 46777 bytes (45 Kb)
opened URL
==================================================
downloaded 45 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/genefilter_1.40.0.tar.gz'
Content type 'application/x-gzip' length 657912 bytes (642 Kb)
opened URL
==================================================
downloaded 642 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/lumi_2.10.0.tar.gz'
Content type 'application/x-gzip' length 10164012 bytes (9.7 Mb)
opened URL
==================================================
downloaded 9.7 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/simpleaffy_2.34.0.tar.gz'
Content type 'application/x-gzip' length 632499 bytes (617 Kb)
opened URL
==================================================
downloaded 617 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/arrayMvout_1.16.0.tar.gz'
Content type 'application/x-gzip' length 586961 bytes (573 Kb)
opened URL
==================================================
downloaded 573 Kb

* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/rgl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
No ability to remove finalizers on externalptr objects in this verison of R
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/XML’
ERROR: dependency ‘rgl’ is not available for package ‘ks’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/ks’
ERROR: dependency ‘XML’ is not available for package ‘annotate’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/annotate’
ERROR: dependency ‘ks’ is not available for package ‘hdrcde’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/hdrcde’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/genefilter’
ERROR: dependencies ‘annotate’, ‘genefilter’ are not available for package ‘methylumi’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/methylumi’
ERROR: dependency ‘genefilter’ is not available for package ‘simpleaffy’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/simpleaffy’
ERROR: dependencies ‘methylumi’, ‘annotate’, ‘hdrcde’ are not available for package ‘lumi’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/lumi’
ERROR: dependencies ‘lumi’, ‘simpleaffy’ are not available for package ‘arrayMvout’
* removing ‘/home/leo/R/x86_64-pc-linux-gnu-library/2.15/arrayMvout’

The downloaded source packages are in
	‘/tmp/Rtmp5PSLNi/downloaded_packages’
There were 11 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘rgl’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘ks’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘annotate’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘hdrcde’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘genefilter’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘methylumi’ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘simpleaffy’ had non-zero exit status
9: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘lumi’ had non-zero exit status
10: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘arrayMvout’ had non-zero exit status
11: installed directory not writable, cannot update packages 'survival


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