Your message dated Wed, 13 Dec 2006 12:48:45 -0600
with message-id <[EMAIL PROTECTED]>
and subject line Bug#402874: r-cran-nlme: package not available to R, although
files are installed
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--- Begin Message ---
Package: r-cran-nlme
Version: 3.1.77-1
Severity: important
After upgrading from sarge to etch:
> library(nlme)
Fehler in library(nlme) : es gibt kein Paket 'nlme'
(in English: there is no package 'nlme').
In the HTML package index, several packages that are installed in
/usr/lib/R/library are not listed.
I am only filing a bug on r-cran-nlme, although at least r-cran-vr and
some other r-cran packages are affected, too.
Let me know if I can help in the diagnosis.
Cheers,
Johannes
-- System Information:
Debian Release: 4.0
APT prefers testing
APT policy: (500, 'testing'), (500, 'stable')
Architecture: amd64 (x86_64)
Shell: /bin/sh linked to /bin/bash
Kernel: Linux 2.6.18-3-xen-amd64
Locale: [EMAIL PROTECTED], [EMAIL PROTECTED] (charmap=ISO-8859-15)
Versions of packages r-cran-nlme depends on:
ii libc6 2.3.6.ds1-8 GNU C Library: Shared libraries
ii r-base-core 2.4.0.20061125-1 GNU R core of statistical computin
ii r-cran-lattice 0.14-13-1 GNU R package for 'Trellis' graphi
r-cran-nlme recommends no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
(Resending, this time with correct BTS address. Sorry for the earlier
mail. --Dirk)
On Wed, Dec 13, 2006 at 11:05:31AM -0600, Dirk Eddelbuettel wrote:
>
> On 13 December 2006 at 17:30, Johannes Ranke wrote:
> | Hi Dirk, Hi Christian (please look at my original bug report)
> |
> | I upgraded current sarge nlme to etch, and have no troubles, although I
> | noted the following output from apt-get dist-upgrade:
> |
> | Preparing to replace r-cran-lattice 0.11-6-1 (using
> .../r-cran-lattice_0.14-13-1_i386.deb) ...
> | Unpacking replacement r-cran-lattice ...
> | /usr/bin/R: line 113: /usr/lib/R/etc/ldpaths: No such file or directory
> | dpkg: warning - old post-removal script returned error exit status 1
> | dpkg - trying script from the new package instead ...
> | dpkg: ... it looks like that went OK.
> | Preparing to replace r-cran-nlme 3.1.55-1 (using
> .../r-cran-nlme_3.1.77-1_i386.deb) ...
> | Unpacking replacement r-cran-nlme ...
> | /usr/bin/R: line 113: /usr/lib/R/etc/ldpaths: No such file or directory
> | dpkg: warning - old post-removal script returned error exit status 1
> | dpkg - trying script from the new package instead ...
> | dpkg: ... it looks like that went OK.
> |
> | But I just now remembered that on the box where the bug occured I
> | upgraded starting from the R 2.4.0 backport of Christian Steigies, which
> | included r-recommended.
>
> Ahhhh. Not a Debian bug then, but a user-error in mixing and switching repos
> which, as you surely understand, we can not fully guarantee as well.
>
> I am sure Christian would welcome your help in making this transition a
> smoother one.
>
> | Looking at his r-recommended package (6.1 MB), it contains, among
> | others, the full nlme package!
> |
> | So I guess the problem is the incompatibility of Christian's packages
> | with the official Debian ones in some way or the other. I have put him
> | in the CC of this mail.
> |
> | Once could expect that the upgrade from an backport works without
> | problems, but not necessarily so. And it seems not to be a bug in the
> | Debian package. So I think the bug can be closed.
>
> Agreed, and bug closed.
>
> Gruesse, Dirk
>
> | Johannes
> |
> | * Dirk Eddelbuettel <[EMAIL PROTECTED]> [061213 17:00]:
> | >
> | > Hi Johannes,
> | >
> | > Thanks for the follow-ups. I'll combine my replies to both mails into this
> | > one.
> | >
> | > On 13 December 2006 at 14:10, Johannes Ranke wrote:
> | > | > Works for me on my testing box with 3.1.77-1 -- see below.
> | > | >
> | > | > Could you please grep for R_LIBS in
> | > | > /etc/R/
> | > |
> | > | jazzy:/etc/R# grep R_LIBS *
> | > |
> Renviron:R_LIBS=${R_LIBS-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
> | > |
> Renviron.dpkg-dist:R_LIBS=${R_LIBS-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
> | > |
> | > | > /usr/lib/R/etc/
> | > |
> | > | jazzy:/usr/lib/R/etc# grep R_LIBS *
> | > |
> Renviron:R_LIBS=${R_LIBS-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
> | >
> | > Defaults, so it finds the package.
> | >
> | > | > and it should come up once in
> | > |
> | > | ???
> | > |
> | > | I had the thought that the help index is not built in the postrm script
> | > | (there are a few lines commented out that would probably do this), but
> | > | this would not explain why the R packages can not be loaded...
> | >
> | > The help index has nothing to do with how library() works. The help index
> | > now gets rebuilt once you say help.start() in R.
> | > |
> | > | > Weird. Let's check -- we obviously need to fix this if it is a
> generic issue.
> | > |
> | > | Yes, definitely. For now I can only use packages installed directly from
> | > | CRAN via install.packages() on this box, or use my Windows XP instance
> in
> | > | Xen which also works nicely ...
> | >
> | > Ah. I still haven't tried Xen, but I do like vmware...
> |
> | Well, I got new hardware (AM2 socket), and could not resist to try Xen.
> | The etch version with kernel 2.6.18 works nicely with windows xp
> | professional (needed for rdesktop connection).
> |
> | Greetings,
> |
> | Johannes
> |
> | >
> | > On 13 December 2006 at 16:06, Johannes Ranke wrote:
> | > | I investigated some more and was able to solve the problem
> | > | by purging (!) r-cran-nlme + r-cran-lattice and reinstalling them.
> | > |
> | > | I am as yet unable to reproduce the problem. I will do another upgrade
> | > | from sarge to etch, and will report if the problem reappears.
> | >
> | > Sounds like a good idea. Please try to note which versions of
> r-cran-nlme et
> | > al you are upgraing from, and to, and under which R version. I may have a
> | > hard time replicating this but I can try ....
> | >
> | > Dirk
> | >
> | > --
> | > Hell, there are no rules here - we're trying to accomplish something.
> | > -- Thomas A. Edison
>
> --
> Hell, there are no rules here - we're trying to accomplish something.
> -- Thomas A. Edison
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
--- End Message ---
