Bug#402874: r-cran-nlme: package not available to R, although files are installed
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 0.14-13-1GNU R package for 'Trellis' graphi r-cran-nlme recommends no packages. -- no debconf information -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#402874: r-cran-nlme: package not available to R, although files are installed
Johannes, On 13 December 2006 at 10:54, Johannes Ranke wrote: | 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'). Works for me on my testing box with 3.1.77-1 -- see below. Could you please grep for R_LIBS in /etc/R/ /usr/lib/R/etc/ and it should come up once in | 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. Weird. Let's check -- we obviously need to fix this if it is a generic issue. | Let me know if I can help in the diagnosis. Here is what I get, cut pasted from Emacs: R version 2.4.0 Patched (2006-11-25 r39997) Copyright (C) 2006 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. if(!exists(baseenv, mode=function)) baseenv - function() NULL options(STERM='iESS', editor='emacsclient') library(nlme) library(help=nlme) Information on package 'nlme' Description: Package: nlme Version: 3.1-77 Date: 2006-09-28 [] Dirk | | 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 0.14-13-1GNU R package for 'Trellis' graphi | | r-cran-nlme recommends no packages. | | -- no debconf information | -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#402874: r-cran-nlme: package not available to R, although files are installed
Hi Dirk,
* Dirk Eddelbuettel [EMAIL PROTECTED] [061213 13:30]:
Johannes,
On 13 December 2006 at 10:54, Johannes Ranke wrote:
| 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').
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'}
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...
| 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.
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 ...
| Let me know if I can help in the diagnosis.
Here is what I get, cut pasted from Emacs:
R version 2.4.0 Patched (2006-11-25 r39997)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
if(!exists(baseenv, mode=function)) baseenv - function() NULL
options(STERM='iESS', editor='emacsclient')
library(nlme)
library(help=nlme)
Information on package 'nlme'
Description:
Package: nlme
Version: 3.1-77
Date: 2006-09-28
[]
Dirk
|
| 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 0.14-13-1GNU R package for 'Trellis'
graphi
|
| r-cran-nlme recommends no packages.
|
| -- no debconf information
|
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
--
To UNSUBSCRIBE, email to [EMAIL PROTECTED]
with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#402874: r-cran-nlme: package not available to R, although files are installed
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. Cheers, Johannes * Dirk Eddelbuettel [EMAIL PROTECTED] [061213 13:30]: Johannes, On 13 December 2006 at 10:54, Johannes Ranke wrote: | 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'). Works for me on my testing box with 3.1.77-1 -- see below. Could you please grep for R_LIBS in /etc/R/ /usr/lib/R/etc/ and it should come up once in | 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. Weird. Let's check -- we obviously need to fix this if it is a generic issue. | Let me know if I can help in the diagnosis. Here is what I get, cut pasted from Emacs: R version 2.4.0 Patched (2006-11-25 r39997) Copyright (C) 2006 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. if(!exists(baseenv, mode=function)) baseenv - function() NULL options(STERM='iESS', editor='emacsclient') library(nlme) library(help=nlme) Information on package 'nlme' Description: Package: nlme Version: 3.1-77 Date: 2006-09-28 [] Dirk | | 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 0.14-13-1GNU R package for 'Trellis' graphi | | r-cran-nlme recommends no packages. | | -- no debconf information | -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#402874: r-cran-nlme: package not available to R, although files are installed
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 sayhelp.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...
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
--
To UNSUBSCRIBE, email to [EMAIL PROTECTED]
with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#402874: r-cran-nlme: package not available to R, although files are installed
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.
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.
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 sayhelp.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
--
To UNSUBSCRIBE, email to [EMAIL PROTECTED]
with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
