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Bug 6244

Summary: bug in the ebuild for dev-lang/R
Product: Gentoo Linux Reporter: kdh <bolter111>
Component: New packagesAssignee: George Shapovalov (RETIRED) <george>
Status: RESOLVED FIXED    
Severity: normal CC: bolter111
Priority: High    
Version: unspecified   
Hardware: x86   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description kdh 2002-08-09 04:30:21 UTC
The ebuild for dev-lang/R installs two files which ought to be the same? 
Ie. /usr/bin/R and /usr/lib/R/bin/R. Unfortunately they're not as 
/usr/bin/R executes nicely whereas /usr/lib/R/bin/R yields the error message

"R_HOME (`/var/tmp/portage/R-1.5.1/image//usr/lib/R') not found"

This has the following implications: automatic updates of additional R 
packages from within R using install.packages() does not work as the 
function install.packages calls /usr/lib/R/bin/R instead of /usr/bin/R

(on a side note: shouldn't R be moved to app-sci?)
Comment 1 George Shapovalov (RETIRED) gentoo-dev 2002-08-10 01:19:45 UTC
Hi kdh

Thanks for the bug report!

Ok, upon the look into both those R's I can tell that these are bash wrappers
that are supposed to invoke R.bin.
The only difference is R_HOME_DIR setting, which gets corrected in one of these
but not the other.

I corrected the ebuild to modify R under /usr/lib/R/bin and to symlink it into
/usr/bin
Please test and report if that solves the problem, I am masking the ebuild for now.

George
Comment 2 kdh 2002-08-19 09:14:20 UTC
I've checked the new ebuild and it does indeed work, eg.
  install.packages("foreign")
does work from within R.

However as I'm not too familiar with the inner workings of gentoo, here is 
what I did in order to reinstall R:
  emerge unmerge R
  emerge rsync
in order to remove R and get the ltest protage tree. Now 
  emerge search R
yields that the present persion availible is 1.4.1. I then edit 
/usr/portage/profiles/package.mask and comment the line dealing with R out. 
Then I do
  emerge R
and it installs R version 1.5.1. However it does not download the source 
files anew - I guess this is normal as the changes have been to the ebuild 
script and not the source .files

kdh
Comment 3 George Shapovalov (RETIRED) gentoo-dev 2002-08-19 19:57:58 UTC
Hi.

Thanks for testing!

Yes, everything you did was correct (you could just emerge it over existing
version, but doing unmerge followed by emerge sometimes can give a cleaner
result (identical in this case)).
As I indicated, ebuild was masked, so you (correctly) unmasked it by commeting
out its entry in the package.mask. Sources are not fetched again since you
already have them. All the modifications introduced by gentoo developers are
indeed stored as patches or parts of ebuilds in your [local] portage database.

I am unmasking the ebuild and closing the bug now after successful testing.

George