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
Hello, would it be possible to make a decision whether this forwarded to the list or declined. Its now 2 days. Thanks Christoph On 31/05/13 14:33, 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? 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 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >