[BioC] Problem installing packages on new R

Thu Feb 14 15:24:44 CET 2013

Hi Vytautas,

On 2/13/2013 5:20 AM, v.leoncikas at surrey.ac.uk wrote:
> 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.

This is problem number 1. You need to have Xorg or another X11 windowing 
system installed. If your computer was set up strictly as a server, then 
X11 might not have been installed. You should talk to your sysadmin 
about installing X11.

> 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

This is problem number 2. You need to have the XML headers available to 
install the XML package. You should talk to your sysadmin about 
installing libxml2-dev.

Best,

Jim

> 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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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099