Hi,
How did you upgraded your version of R? From source or from a Linux package?
Regards,
Pascal
On 05/31/2013 11:33 AM, Christoph Knapp wrote:
Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
realized that I have to update all the installed packages so I run >
update.packages(checkBuilt=TRUE)
as described here
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
. The first thing it did was telling me that it will not update several
packages. When it was finished I used the warnings function to have a
look at what did not work. See the list below.
> warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
I tried to reinstall them manually but this always failed because of a
package dependency to the "compiler" package. Now, if I try to install
the compiler package it tells me.
> install.packages("compiler")
Installing package into ?/home/christoph/R/x86_64-pc-linux-gnu-library/3.0?
(as ?lib? is unspecified)
Warning message:
package ?compiler? is not available (for R version 3.0.1)
The last line also came up all the time when the packages were updated
Doing a bit of research does not deliver much only that the compiler
package was included into R at version 2.13.0
(http://dirk.eddelbuettel.com/blog/2011/04/12/).
Most of those packages which do not work any more are pretty important
for some of my scripts and I would not even know what packages replace
the packages above.
Would anyone know how to fix this?
Regards
Hi,
How did you upgraded your version of R? From source or from a Linux
package?
Actually the new R installation is just broken. It simply has to be
reinstalled carefully (watch for errors).
Best,
Uwe Ligges
Regards,
Pascal
On 05/31/2013 11:33 AM, Christoph Knapp wrote:
Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
realized that I have to update all the installed packages so I run >
update.packages(checkBuilt=TRUE)
as described here
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
. The first thing it did was telling me that it will not update several
packages. When it was finished I used the warnings function to have a
look at what did not work. See the list below.
> warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
I tried to reinstall them manually but this always failed because of a
package dependency to the "compiler" package. Now, if I try to install
the compiler package it tells me.
> install.packages("compiler")
Installing package into
?/home/christoph/R/x86_64-pc-linux-gnu-library/3.0?
(as ?lib? is unspecified)
Warning message:
package ?compiler? is not available (for R version 3.0.1)
The last line also came up all the time when the packages were updated
Doing a bit of research does not deliver much only that the compiler
package was included into R at version 2.13.0
(http://dirk.eddelbuettel.com/blog/2011/04/12/).
Most of those packages which do not work any more are pretty important
for some of my scripts and I would not even know what packages replace
the packages above.
Would anyone know how to fix this?
Regards
Hi,
How did you upgraded your version of R? From source or from a Linux
package?
Actually the new R installation is just broken. It simply has to be
reinstalled carefully (watch for errors).
Best,
Uwe Ligges
Regards,
Pascal
On 05/31/2013 11:33 AM, Christoph Knapp wrote:
Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
realized that I have to update all the installed packages so I run >
update.packages(checkBuilt=TRUE)
as described here
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
. The first thing it did was telling me that it will not update several
packages. When it was finished I used the warnings function to have a
look at what did not work. See the list below.
> warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
I tried to reinstall them manually but this always failed because of a
package dependency to the "compiler" package. Now, if I try to install
the compiler package it tells me.
> install.packages("compiler")
Installing package into
?/home/christoph/R/x86_64-pc-linux-gnu-library/3.0?
(as ?lib? is unspecified)
Warning message:
package ?compiler? is not available (for R version 3.0.1)
The last line also came up all the time when the packages were updated
Doing a bit of research does not deliver much only that the compiler
package was included into R at version 2.13.0
(http://dirk.eddelbuettel.com/blog/2011/04/12/).
Most of those packages which do not work any more are pretty important
for some of my scripts and I would not even know what packages replace
the packages above.
Would anyone know how to fix this?
Regards
Hi,
reinstalling R did not help. It still will not update the same packages.
I attached the terminal output. There were no errors while I was
installing R again. I might have to remove all libraries and reinstall
them all. Would you agree or do you think I should try something else
first which is not as extreme.
Thanks for your help
Christoph
On 03/06/13 20:32, Pascal Oettli wrote:
My mistake,
Regards,
Pascal
On 06/03/2013 04:37 PM, Uwe Ligges wrote:
On 03.06.2013 07:19, Pascal Oettli wrote:
Hi,
How did you upgraded your version of R? From source or from a Linux
package?
Actually the new R installation is just broken. It simply has to be
reinstalled carefully (watch for errors).
Best,
Uwe Ligges
Regards,
Pascal
On 05/31/2013 11:33 AM, Christoph Knapp wrote:
Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
realized that I have to update all the installed packages so I run >
update.packages(checkBuilt=TRUE)
as described here
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
. The first thing it did was telling me that it will not update
several
packages. When it was finished I used the warnings function to have a
look at what did not work. See the list below.
> warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
I tried to reinstall them manually but this always failed because of a
package dependency to the "compiler" package. Now, if I try to install
the compiler package it tells me.
> install.packages("compiler")
Installing package into
?/home/christoph/R/x86_64-pc-linux-gnu-library/3.0?
(as ?lib? is unspecified)
Warning message:
package ?compiler? is not available (for R version 3.0.1)
The last line also came up all the time when the packages were updated
Doing a bit of research does not deliver much only that the compiler
package was included into R at version 2.13.0
(http://dirk.eddelbuettel.com/blog/2011/04/12/).
Most of those packages which do not work any more are pretty important
for some of my scripts and I would not even know what packages replace
the packages above.
Would anyone know how to fix this?
Regards
-------------- next part --------------
christoph at christoph-Latitude-E4300:~$ sudo apt-get --purge remove r-base-core
[sudo] password for christoph:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED
r-base* r-base-core* r-base-dev* r-base-html* r-cran-boot* r-cran-class*
r-cran-cluster* r-cran-codetools* r-cran-foreign* r-cran-kernsmooth*
r-cran-lattice* r-cran-mass* r-cran-matrix* r-cran-mgcv* r-cran-nlme*
r-cran-nnet* r-cran-rpart* r-cran-spatial* r-cran-survival* r-recommended*
0 upgraded, 0 newly installed, 20 to remove and 20 not upgraded.
After this operation, 51.5 MB disk space will be freed.
Do you want to continue [Y/n]? Y
(Reading database ... 429389 files and directories currently installed.)
Removing r-base ...
Removing r-recommended ...
Removing r-cran-boot ...
Removing r-cran-mgcv ...
Removing r-cran-matrix ...
Removing r-cran-rpart ...
Removing r-cran-survival ...
Removing r-cran-kernsmooth ...
Removing r-base-dev ...
Removing r-cran-spatial ...
Removing r-cran-cluster ...
Removing r-cran-class ...
Removing r-cran-foreign ...
Removing r-cran-nlme ...
Removing r-cran-nnet ...
Removing r-base-html ...
Removing r-cran-lattice ...
Removing r-cran-mass ...
Removing r-cran-codetools ...
Removing r-base-core ...
Purging configuration files for r-base-core ...
dpkg: warning: while removing r-base-core, directory '/usr/lib/R/library' not empty so not removed.
dpkg: warning: while removing r-base-core, directory '/usr/lib/R/site-library' not empty so not removed.
Processing triggers for man-db ...
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf.index...
Processing triggers for desktop-file-utils ...
Processing triggers for gnome-menus ...
Processing triggers for hicolor-icon-theme ...
Processing triggers for install-info ...
christoph at christoph-Latitude-E4300:~$ R
The program 'R' is currently not installed. You can install it by typing:
sudo apt-get install r-base-core
christoph at christoph-Latitude-E4300:~$ sudo apt-get install r-base-core
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme
r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended
Suggested packages:
ess r-doc-info r-doc-pdf r-mathlib r-base-html texinfo texi2html
The following NEW packages will be installed
r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools
r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended
0 upgraded, 18 newly installed, 0 to remove and 20 not upgraded.
Need to get 0 B/35.6 MB of archives.
After this operation, 50.8 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
Selecting previously unselected package r-base-core.
(Reading database ... 427503 files and directories currently installed.)
Unpacking r-base-core (from .../r-base-core_3.0.1-3precise_amd64.deb) ...
Selecting previously unselected package r-base-dev.
Unpacking r-base-dev (from .../r-base-dev_3.0.1-3precise_all.deb) ...
Selecting previously unselected package r-cran-boot.
Unpacking r-cran-boot (from .../r-cran-boot_1.3-9-1precise0_all.deb) ...
Selecting previously unselected package r-cran-mass.
Unpacking r-cran-mass (from .../r-cran-mass_7.3-26-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-class.
Unpacking r-cran-class (from .../r-cran-class_7.3-7-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-cluster.
Unpacking r-cran-cluster (from .../r-cran-cluster_1.14.4-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-codetools.
Unpacking r-cran-codetools (from .../r-cran-codetools_0.2-8-2precise0_all.deb) ...
Selecting previously unselected package r-cran-foreign.
Unpacking r-cran-foreign (from .../r-cran-foreign_0.8.54-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-kernsmooth.
Unpacking r-cran-kernsmooth (from .../r-cran-kernsmooth_2.23-10-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-lattice.
Unpacking r-cran-lattice (from .../r-cran-lattice_0.20-15-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-matrix.
Unpacking r-cran-matrix (from .../r-cran-matrix_1.0-12-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-nlme.
Unpacking r-cran-nlme (from .../r-cran-nlme_3.1.109-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-mgcv.
Unpacking r-cran-mgcv (from .../r-cran-mgcv_1.7-23-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-nnet.
Unpacking r-cran-nnet (from .../r-cran-nnet_7.3-6-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-survival.
Unpacking r-cran-survival (from .../r-cran-survival_2.37-4-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-rpart.
Unpacking r-cran-rpart (from .../r-cran-rpart_4.1-1-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-spatial.
Unpacking r-cran-spatial (from .../r-cran-spatial_7.3-6-1precise0_amd64.deb) ...
Selecting previously unselected package r-recommended.
Unpacking r-recommended (from .../r-recommended_3.0.1-3precise_all.deb) ...
Processing triggers for install-info ...
Processing triggers for hicolor-icon-theme ...
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf.index...
Processing triggers for desktop-file-utils ...
Processing triggers for gnome-menus ...
Processing triggers for man-db ...
Setting up r-base-core (3.0.1-3precise) ...
Creating config file /etc/R/Renviron with new version
mktexlsr: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
mktexlsr: Done.
Setting up r-base-dev (3.0.1-3precise) ...
Setting up r-cran-boot (1.3-9-1precise0) ...
Setting up r-cran-mass (7.3-26-1precise0) ...
Setting up r-cran-class (7.3-7-1precise0) ...
Setting up r-cran-cluster (1.14.4-1precise0) ...
Setting up r-cran-codetools (0.2-8-2precise0) ...
Setting up r-cran-foreign (0.8.54-1precise0) ...
Setting up r-cran-kernsmooth (2.23-10-2precise0) ...
Setting up r-cran-lattice (0.20-15-1precise0) ...
Setting up r-cran-matrix (1.0-12-1precise0) ...
Setting up r-cran-nlme (3.1.109-1precise0) ...
Setting up r-cran-mgcv (1.7-23-1precise0) ...
Setting up r-cran-nnet (7.3-6-2precise0) ...
Setting up r-cran-survival (2.37-4-2precise0) ...
Setting up r-cran-rpart (4.1-1-2precise0) ...
Setting up r-cran-spatial (7.3-6-1precise0) ...
Setting up r-recommended (3.0.1-3precise) ...
christoph at christoph-Latitude-E4300:~$
christoph at christoph-Latitude-E4300:~$ sudo R
R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
Natural language support but running in an English locale
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.
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
Hi Christoph,
do you install from sources?
Best
Simon
On Jun 4, 2013, at 10:41 AM, Christoph Knapp <christoph.knapp01 at gmail.com> wrote:
Hi,
reinstalling R did not help. It still will not update the same packages. I attached the terminal output. There were no errors while I was installing R again. I might have to remove all libraries and reinstall them all. Would you agree or do you think I should try something else first which is not as extreme.
Thanks for your help
Christoph
On 03/06/13 20:32, Pascal Oettli wrote:
My mistake,
Regards,
Pascal
On 06/03/2013 04:37 PM, Uwe Ligges wrote:
On 03.06.2013 07:19, Pascal Oettli wrote:
Hi,
How did you upgraded your version of R? From source or from a Linux
package?
Actually the new R installation is just broken. It simply has to be
reinstalled carefully (watch for errors).
Best,
Uwe Ligges
Regards,
Pascal
On 05/31/2013 11:33 AM, Christoph Knapp wrote:
Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
realized that I have to update all the installed packages so I run >
update.packages(checkBuilt=TRUE)
as described here
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
. The first thing it did was telling me that it will not update several
packages. When it was finished I used the warnings function to have a
look at what did not work. See the list below.
warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
I tried to reinstall them manually but this always failed because of a
package dependency to the "compiler" package. Now, if I try to install
the compiler package it tells me.
install.packages("compiler")
Installing package into
?/home/christoph/R/x86_64-pc-linux-gnu-library/3.0?
(as ?lib? is unspecified)
Warning message:
package ?compiler? is not available (for R version 3.0.1)
The last line also came up all the time when the packages were updated
Doing a bit of research does not deliver much only that the compiler
package was included into R at version 2.13.0
(http://dirk.eddelbuettel.com/blog/2011/04/12/).
Most of those packages which do not work any more are pretty important
for some of my scripts and I would not even know what packages replace
the packages above.
Would anyone know how to fix this?
Regards
Usually sudo apt-get install ... Sometimes synaptic package manager. I'm
using the
So you really do need to discuss this on R-sig-debian, as those OSes
have their own non-R package layout.
Do not expect the R manuals to cover the changes made by third-party
re-distributors, nor advice by general R users nor R bloggers.
/http://cran.ma.imperial.ac.uk/bin/linux/ubuntu/precise/http://cran.stat.ucla.edu/bin/linux/ubuntu/precise
repositories. Not sure what the differences are. I had some problems
before when I installed packages from within Rstudio. It would install
them in a different directory than apt-get would and it would tell me
that those packages were not installed when I used the terminal to start
R. Drove me crazy for a while because I could use them in Rstudio so I
was sure they were installed. Do you think this could also cause this?
Christoph
/
On 04/06/13 21:13, Simon Zehnder wrote:
Hi Christoph,
do you install from sources?
Best
Simon
On Jun 4, 2013, at 10:41 AM, Christoph Knapp <christoph.knapp01 at gmail.com> wrote:
Hi,
reinstalling R did not help. It still will not update the same packages. I attached the terminal output. There were no errors while I was installing R again. I might have to remove all libraries and reinstall them all. Would you agree or do you think I should try something else first which is not as extreme.
Thanks for your help
Christoph
On 03/06/13 20:32, Pascal Oettli wrote:
My mistake,
Regards,
Pascal
On 06/03/2013 04:37 PM, Uwe Ligges wrote:
On 03.06.2013 07:19, Pascal Oettli wrote:
Hi,
How did you upgraded your version of R? From source or from a Linux
package?
Actually the new R installation is just broken. It simply has to be
reinstalled carefully (watch for errors).
Best,
Uwe Ligges
Regards,
Pascal
On 05/31/2013 11:33 AM, Christoph Knapp wrote:
Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
realized that I have to update all the installed packages so I run >
update.packages(checkBuilt=TRUE)
as described here
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
. The first thing it did was telling me that it will not update several
packages. When it was finished I used the warnings function to have a
look at what did not work. See the list below.
warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
I tried to reinstall them manually but this always failed because of a
package dependency to the "compiler" package. Now, if I try to install
the compiler package it tells me.
install.packages("compiler")
Installing package into
?/home/christoph/R/x86_64-pc-linux-gnu-library/3.0?
(as ?lib? is unspecified)
Warning message:
package ?compiler? is not available (for R version 3.0.1)
The last line also came up all the time when the packages were updated
Doing a bit of research does not deliver much only that the compiler
package was included into R at version 2.13.0
(http://dirk.eddelbuettel.com/blog/2011/04/12/).
Most of those packages which do not work any more are pretty important
for some of my scripts and I would not even know what packages replace
the packages above.
Would anyone know how to fix this?
Regards
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
Hi,
Did you try:
update.packages(installed.packages()[,1])
or
install.packages(installed.packages()[,1])
This will reinstall the packages you have on your system and for which
updates for 3.0.1 exist.
In my experience, as recounted here earlier, update.packages()
does not always work: it breaks because it fails to also recognize the
need to update some dependencies.
If reducing bandwidth is your concern, you can update the ones that
did not update manually, but note that this is a long drawn process
with one dependency leading to another in many cases.
All this is from my experience of updating R 2.15.2 to R 3.0.0 and
later R 3.0.1: of course YMMV.
HTH,
Ranjan
On Tue, 4 Jun 2013 20:41:21 +1200 Christoph Knapp
<christoph.knapp01 at gmail.com> wrote:
Hi,
reinstalling R did not help. It still will not update the same packages.
I attached the terminal output. There were no errors while I was
installing R again. I might have to remove all libraries and reinstall
them all. Would you agree or do you think I should try something else
first which is not as extreme.
Thanks for your help
Christoph
On 03/06/13 20:32, Pascal Oettli wrote:
My mistake,
Regards,
Pascal
On 06/03/2013 04:37 PM, Uwe Ligges wrote:
On 03.06.2013 07:19, Pascal Oettli wrote:
Hi,
How did you upgraded your version of R? From source or from a Linux
package?
Actually the new R installation is just broken. It simply has to be
reinstalled carefully (watch for errors).
Best,
Uwe Ligges
Regards,
Pascal
On 05/31/2013 11:33 AM, Christoph Knapp wrote:
Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
realized that I have to update all the installed packages so I run >
update.packages(checkBuilt=TRUE)
as described here
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
. The first thing it did was telling me that it will not update
several
packages. When it was finished I used the warnings function to have a
look at what did not work. See the list below.
> warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?boot? had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?cluster? had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?foreign? had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?KernSmooth? had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?MASS? had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?Matrix? had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nlme? had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?nnet? had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?rpart? had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?spatial? had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?survival? had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?class? had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?epiR? had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gmodels? had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gplots? had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?mgcv? had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ?gregmisc? had non-zero exit status
I tried to reinstall them manually but this always failed because of a
package dependency to the "compiler" package. Now, if I try to install
the compiler package it tells me.
> install.packages("compiler")
Installing package into
?/home/christoph/R/x86_64-pc-linux-gnu-library/3.0?
(as ?lib? is unspecified)
Warning message:
package ?compiler? is not available (for R version 3.0.1)
The last line also came up all the time when the packages were updated
Doing a bit of research does not deliver much only that the compiler
package was included into R at version 2.13.0
(http://dirk.eddelbuettel.com/blog/2011/04/12/).
Most of those packages which do not work any more are pretty important
for some of my scripts and I would not even know what packages replace
the packages above.
Would anyone know how to fix this?
Regards
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