Hi,
from the message
install.packages(pkgs = "aws", type = "source", lib =
"/home/cathy/R/i486-pc-linux-gnu-library/2.6"...
it looks like you have some really old settings hanging around, e.g.
R_LIBS. What does
print(.libPaths())
report?
Check Sys.getenv("R_LIBS"), it might be set in your ~/.bash_profile or
in your ~/.Renviron file.
Also, troubleshoot, by verifying that you can install, say the 'aws'
package (on CRAN) manually, e.g. does the following work?
install.packages("aws")
If you cannot get the latter to work, ask for help on the r-help mailing list.
/Henrik
On Tue, Jun 9, 2009 at 5:32 AM, Cathy
Mitchell<cathrinemitch...@gmail.com> wrote:
> Hi
> I am having some problems downloading aroma.affymetrix on my linux machine.
> It downloaded fine on my windows machine. I am running ubuntu (hardy heron v
> 8.04) on my laptop. I have R version 2.9.0.
>
> I used:
> source("http://www.braju.com/R/hbLite.R";)
> hbInstall("aroma.affymetrix")
>
> I get the following:
>
> ############################################################
>
> # #
>
> # Packages installed/updated. Please restart R. #
>
> # #
>
> ############################################################
>
> There were 39 warnings (use warnings() to see them)
>
>> warnings()
>
> Warning messages:
>
> 1: In install.packages(pkgs = "aroma.apd", type = "source", ... :
>
> installation of package 'aroma.apd' had non-zero exit status
>
> 2: In packageDescription(pkg) : no package 'affxparser' was found
>
> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'affxparser' had non-zero exit status
>
> 4: In packageDescription(pkg) : no package 'preprocessCore' was found
>
> 5: In safeSource() : Redefining
>
> 6: In safeSource() : Redefining
>
> 7: In safeSource() : Redefining
>
> 8: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'preprocessCore' had non-zero exit status
>
> 9: In packageDescription(pkg) : no package 'gcrma' was found
>
> 10: In safeSource() : Redefining
>
> 11: In safeSource() : Redefining
>
> 12: In safeSource() : Redefining
>
> 13: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'preprocessCore' had non-zero exit status
>
> 14: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'affy' had non-zero exit status
>
> 15: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'gcrma' had non-zero exit status
>
> 16: In packageDescription(pkg) : no package 'affy' was found
>
> 17: In safeSource() : Redefining
>
> 18: In safeSource() : Redefining
>
> 19: In safeSource() : Redefining
>
> 20: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'preprocessCore' had non-zero exit status
>
> 21: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'affy' had non-zero exit status
>
> 22: In packageDescription(pkg) : no package 'matchprobes' was found
>
> 23: In safeSource() : Redefining
>
> 24: In safeSource() : Redefining
>
> 25: In safeSource() : Redefining
>
> 26: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'preprocessCore' had non-zero exit status
>
> 27: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'affy' had non-zero exit status
>
> 28: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'matchprobes' had non-zero exit status
>
> 29: In install.packages(pkgs = "aws", type = "source", lib =
> "/home/cathy/R/i486-pc-linux-gnu-library/2.6", ... :
>
> installation of package 'aws' had non-zero exit status
>
> 30: In packageDescription(pkg) : no package 'GLAD' was found
>
> 31: In safeSource() : Redefining
>
> 32: In safeSource() : Redefining
>
> 33: In safeSource() : Redefining
>
> 34: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'GLAD' had non-zero exit status
>
> 35: In packageDescription(pkg) : no package 'DNAcopy' was found
>
> 36: In safeSource() : Redefining
>
> 37: In safeSource() : Redefining
>
> 38: In safeSource() : Redefining
>
> 39: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>
> installation of package 'DNAcopy' had non-zero exit status
>
> When I restart R and call:
>
> library('aroma.affymetrix')
> it says there is no such package installed.
>
> I would really appreciate it if you could give me some pointers as to where
> I am going wrong.
>
> thank you very much.
>
>
>
> --
> Cathrine Mitchell
>
>
> >
>
--~--~---------~--~----~------------~-------~--~----~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
