Hej

I am reinstalling bioconductor because I needed to reinstall my OS due to some complications and I am experiencing some complications.

I cannot install some of the packages and get this output at the end

The downloaded source packages are in
    ‘/tmp/Rtmpn4Uw0m/downloaded_packages’
Warning message:
installed directory not writable, cannot update packages 'affy',
  'affyio', 'AnnotationDbi', 'Biobase', 'BiocInstaller', 'biovizBase',
  'chron', 'colorspace', 'DBI', 'digest', 'fastcluster', 'Formula',
  'GenomicFeatures', 'GenomicRanges', 'ggplot2', 'graph', 'Hmisc',
  'hwriter', 'hypergraph', 'IRanges', 'labeling', 'limma',
  'makecdfenv', 'plyr', 'preprocessCore', 'RColorBrewer', 'RCurl',
  'reshape2', 'Rsamtools', 'RSQLite', 'rtracklayer', 'scales',
  'statmod', 'tcltk2', 'tgp', 'cluster', 'lattice', 'MASS', 'rpart' 

Any ideas what the problem is ??

Are you using a personal computer or one belonging to the institute? Do you have admin privileges on R?

I am using a personal computer, how do I check if I have admin privileges on R?

I tried sudo R and then installing affy for example and it seems to be working.

So basically I installed R, without admin privilages, how is that even possible when I used sudo apt-get install?

Do you think you could tell me how I can change the admin privilages. I am only running linux mint on this computer if that makes a difference.

I have another problem now with installing OneChannelGUI, I get this error when it is installing:

ucsc/zlibFace.c:4:18: fatal error: zlib.h: No such file or directory
 #include <zlib.h>

these are my warnings

1: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘tkrplot’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘affyPLM’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘affylmGUI’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘oneChannelGUI’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘affyio’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘preprocessCore’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘RCurl’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Rsamtools’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘statmod’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘tgp’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘rtracklayer’ had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘GenomicFeatures’ had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘cluster’ had non-zero exit status

I can make another thread if no one asnwers it

thanks

I finally managed to figure it out. Linux mint has an older version in its dependencies, so I had to purge everything and reinstall the newer version. Then reinstall many packages that don't install automatically.

I am still not able to install Rcurl, but I can run bioconductor so no worries I guess

Thanks for the help