Question: warning directory not writable
0
gravatar for Eric P
4.8 years ago by
Eric P10
Sweden
Eric P10 wrote:

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 ??

installation • 1.7k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Eric P10
Answer: warning directory not writable
0
gravatar for Patrick Schorderet
4.8 years ago by
United States
Patrick Schorderet20 wrote:

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

ADD COMMENTlink written 4.8 years ago by Patrick Schorderet20
Answer: warning directory not writable
0
gravatar for Eric P
4.8 years ago by
Eric P10
Sweden
Eric P10 wrote:

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

ADD COMMENTlink modified 4.8 years ago by Martin Morgan ♦♦ 24k • written 4.8 years ago by Eric P10

You are becoming a super user (administrator) when you said sudo ... so that you installed R as administrator, Probably the best thing to do is install base R in this way, but then install other packages as a regular user with biocLite(). For the first package, R will ask whether you wish to create a personal directory. Install all packages there, where you will have correct write permissions.

The error above looks like your system is unable to find zlib.h. It is a little surprising (to me as a non-mint user) that this is not available in your base system, so it might pay to investigate further. But I think you can solve this with sudo apt-get install zlib1g-dev.

ADD REPLYlink written 4.8 years ago by Martin Morgan ♦♦ 24k
Answer: warning directory not writable
0
gravatar for Eric P
4.8 years ago by
Eric P10
Sweden
Eric P10 wrote:

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

ADD COMMENTlink written 4.8 years ago by Eric P10

Likely you see a similar message about missing <curl.h>. Use sudo apt-get install libcurl4-openssl-dev (and likely also libxml2-dev).

ADD REPLYlink written 4.8 years ago by Martin Morgan ♦♦ 24k
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