Hi! As per Thomas' advice, I upgraded R by using "update.packages()" and got the following warning messages: Warning messages: 1: installation of package 'lmtest' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, 2: installation of package 'quadprog' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, 3: installation of package 'cluster' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, 4: installation of package 'tseries' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, Do I need to worry about these messages? Do I need to do something else to complete the upgrade process? Another question: what is the command for renaming an existing variable? Thanks. Deepankar
On Tue, 19 Dec 2006, DEEPANKAR BASU wrote:> Hi! > > As per Thomas' advice, I upgraded R by using "update.packages()" and got > the following warning messages:That was not my advice on how to upgrade. update.packages() updates the packages. You need to download a new version of R itself. You will then need to update or reinstall the packages. The warning messages are because you are updating to versions of the packages that do not run on your old version of R. -thomas> Warning messages: > 1: installation of package 'lmtest' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, > 2: installation of package 'quadprog' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, > 3: installation of package 'cluster' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, > 4: installation of package 'tseries' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, > > Do I need to worry about these messages? Do I need to do something else to complete the upgrade process? > > Another question: what is the command for renaming an existing variable? > > Thanks. > Deepankar > > ______________________________________________ > R-help at stat.math.ethz.ch 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. >Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle
Hi as the addition to Thomas's answer. On 19 Dec 2006 at 15:20, Thomas Lumley wrote: Date sent: Tue, 19 Dec 2006 15:20:18 -0800 (PST) From: Thomas Lumley <tlumley at u.washington.edu> To: DEEPANKAR BASU <basu.15 at osu.edu> Copies to: R-help at stat.math.ethz.ch Subject: Re: [R] Upgrading> On Tue, 19 Dec 2006, DEEPANKAR BASU wrote: > > > Hi! > > > > As per Thomas' advice, I upgraded R by using "update.packages()" and > > got the following warning messages: > > That was not my advice on how to upgrade. update.packages() updates > the packages. You need to download a new version of R itself. You > will then need to update or reinstall the packages. The warning > messages are because you are updating to versions of the packages that > do not run on your old version of R.<snip>> > > > Another question: what is the command for renaming an existing > > variable?e.g. if the variable is in data frame names(your.data)[position.of.old.column.name] <- "new.column.name" BTW, reading et least some docummentation could help you a lot with these issues. HTH Petr> > > > Thanks. > > Deepankar > > > > ______________________________________________ > > R-help at stat.math.ethz.ch 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. > > > > Thomas Lumley Assoc. Professor, Biostatistics > tlumley at u.washington.edu University of Washington, Seattle > > ______________________________________________ > R-help at stat.math.ethz.ch 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.Petr Pikal petr.pikal at precheza.cz
Thanks for the comments. I had got Thomas' message wrong the first time. Now, I have downloaded and re-installed the latest version of R. After reading the "administration and maintenance" manual, I added deb http://cran.R-project.org/bin/linux/ubuntu dapper/ to my sources.list file and used apt-get to install the latest version. After the installation, I used update.packages() from with R to update all the packages. Let me know if this was what was required or I made some mistake. I have two questions: 1. When a new version of R is released (every 6 months or so I believe) will I have to uninstall the version of R in my machine and then download and install the latest version? 2. When I used update.packages() from within R (after installing the latest version), I still got the following warning messages: Warning messages: 1: installation of package 'cluster' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, 2: installation of package 'mgcv' had non-zero exit status in: install.packages(update[, "Package"], instlib, contriburl = contriburl, 3: cannot create HTML package index in: tools:::unix.packages.html(.Library) I cannot understand what to make of these? Thanks for all the help. Deepankar ----- Original Message ----- From: Petr Pikal <petr.pikal at precheza.cz> Date: Wednesday, December 20, 2006 4:47 am Subject: Re: [R] Upgrading> Hi > > as the addition to Thomas's answer. > > On 19 Dec 2006 at 15:20, Thomas Lumley wrote: > > Date sent: Tue, 19 Dec 2006 15:20:18 -0800 (PST) > From: Thomas Lumley <tlumley at u.washington.edu> > To: DEEPANKAR BASU <basu.15 at osu.edu> > Copies to: R-help at stat.math.ethz.ch > Subject: Re: [R] Upgrading > > > On Tue, 19 Dec 2006, DEEPANKAR BASU wrote: > > > > > Hi! > > > > > > As per Thomas' advice, I upgraded R by using > "update.packages()" and > > > got the following warning messages: > > > > That was not my advice on how to upgrade. update.packages() updates > > the packages. You need to download a new version of R itself. You > > will then need to update or reinstall the packages. The warning > > messages are because you are updating to versions of the packages > that> do not run on your old version of R. > > <snip> > > > > > > > Another question: what is the command for renaming an existing > > > variable? > > e.g. if the variable is in data frame > > names(your.data)[position.of.old.column.name] <- "new.column.name" > BTW, reading et least some docummentation could help you a lot with > these issues. > > HTH > Petr > > > > > > > > Thanks. > > > Deepankar > > > > > > ______________________________________________ > > > R-help at stat.math.ethz.ch 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. > > > > > > > Thomas Lumley Assoc. Professor, Biostatistics > > tlumley at u.washington.edu University of Washington, Seattle > > > > ______________________________________________ > > R-help at stat.math.ethz.ch 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. > > Petr Pikal > petr.pikal at precheza.cz > >
Thanks for the suggestions; they resolved the problems. First I installed r-base-dev and then started R via sudo R. Now, when I used update.packages(), the process completed without any warning messages. Deepankar ----- Original Message ----- From: Ivailo Stoyanov <istoyanov at ecolab.bas.bg> Date: Thursday, December 21, 2006 2:53 am Subject: Re: [R] Upgrading> On Wed, 2006-12-20 at 11:37 -0500, DEEPANKAR BASU wrote: > > Thanks for the comments. I had got Thomas' message wrong the > first time. Now, I have downloaded and re-installed the latest > version of R. After reading the "administration and maintenance" > manual, I added > > > > deb http://cran.R-project.org/bin/linux/ubuntu dapper/ > > > > to my sources.list file and used apt-get to install the latest > version. After the installation, I used update.packages() from with > R to update all the packages. Let me know if this was what was > required or I made some mistake. > > > > I have two questions: > > 1. When a new version of R is released (every 6 months or so I > believe) will I have to uninstall the version of R in my machine > and then download and install the latest version? > > 2. When I used update.packages() from within R (after installing > the latest version), I still got the following warning messages: > > > > Warning messages: > > 1: installation of package 'cluster' had non-zero exit status in: > install.packages(update[, "Package"], instlib, contriburl = > contriburl,> 2: installation of package 'mgcv' had non-zero exit > status in: install.packages(update[, "Package"], instlib, > contriburl = contriburl, > > 3: cannot create HTML package index in: > tools:::unix.packages.html(.Library) > The "cannot create HTML package index" message hints toward > insufficientprivileges -- during "update.packages()" R should run > with administrator > privileges, so you have to start it via "sudo R". The reason for the > other error messages could be also unavailable source packages due to > interrupted network connectivity, but generally the best approach > is to > set up a larger number of scrollback lines in the terminal (the > defaultcould be insufficient) and to inspect the output for the > specific reason > for the "non-zero exit status". Please note, that you may also need > r-base-dev (along with some other) installed in order to successfully > compile any of the packages available at CRAN. > > HTH, > Ivailo > >
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