For some reason, update.packages(), one of the greatest features of R,
doesn''t
work anymore (perhaps since I upgraded to 1.2.1?). It downloads the new
packages, but when it tries to build them, I get this message:
WARNING: ignoring environment value of R_HOME
/var/tmp/R-base-root/usr/lib/R/bin/Rcmd:
/var/tmp/R-base-root/usr/lib/R/bin/Rcmd: No such file or directory
I save the downloaded packages and then do R INSTALL <pkgname> at the
command
line, and it works fine. I tried setting lib=/usr/lib/R and also the R_HOME
environment var, but that didn''t help. What am I doing wrong?
I''m running R 1.2.1 on RedHat Linux 7 (intel).
______________________________________________________________________
Stuart Luppescu -=-=- University of Chicago
$(B:MJ8$HCRF`H~$NIc(B -=-=- s-luppescu at uchicago.edu
http://www.consortium-chicago.org/people/sl.html
http://musuko.uchicago.edu/pubkey.asc for PGP Public Key
ICQ #21172047 AIM: psycho7070
QOTD:
I looked out my window, and saw Kyle Pettys'' car upside down,
then I thought ''One of us is in real trouble''.
-- Davey Allison, on a 150 m.p.h. crash>> Sent on 24-Jan-2001 at 11:58:45 with xfmail
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s-luppescu at uchicago.edu writes:> For some reason, update.packages(), one of the greatest features of R, doesn''t > work anymore (perhaps since I upgraded to 1.2.1?). It downloads the new > packages, but when it tries to build them, I get this message: > > WARNING: ignoring environment value of R_HOME > /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: > /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: No such file or directory > > I save the downloaded packages and then do R INSTALL <pkgname> at the command > line, and it works fine. I tried setting lib=/usr/lib/R and also the R_HOME > environment var, but that didn''t help. What am I doing wrong?What does "R RHOME" tell you? Is R_HOME set in the environment? If so, try removing it. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /''_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
I have R-1.2.1 on a RH-7.0 system and update.packages() seems to work fine form me. I have to admit that I have never used it before. Indeed it is a great feature. Now, I do not have R_HOME defined in my regular bash environment. I simply installed R in my home directory and copied the R shell script to $HOME/bin which is of course on my search path. Here is what I got when I typed update.packages()> update.packages()--13:52:07-- http://cran.r-project.org:80/src/contrib/PACKAGES => `/tmp/fileR4839S238e1f29'' Connecting to cran.r-project.org:80... connected! HTTP request sent, awaiting response... 200 OK Length: 35,419 [text/plain] 0K -> .......... .......... .......... .... [100%] 13:52:08 (46.49 KB/s) - `/tmp/fileR4839S238e1f29'' saved [35419/35419] Matrix : Version 0.3-7 in /home/andyj/stat/R-1.2.1/library Version 0.3-8 on CRAN Update (y/N)? y --13:52:14-- http://cran.r-project.org:80/src/contrib/Matrix_0.3-8.tar.gz => `/tmp/RinstdirR4839S46e87ccd/Matrix_0.3-8.tar.gz'' Connecting to cran.r-project.org:80... connected! HTTP request sent, awaiting response... 200 OK Length: 98,349 [application/x-tar] 0K -> .......... .......... .......... .......... .......... [ 52%] 50K -> .......... .......... .......... .......... ...... [100%] 13:52:16 (67.26 KB/s) - `/tmp/RinstdirR4839S46e87ccd/Matrix_0.3-8.tar.gz'' saved [98349/98349] Installing source package `Matrix'' ... creating cache ./config.cache checking for gcc... gcc ... compilation output snipped .... R data help >>> Building/Updating help pages for package `Matrix'' Formats: text html latex example DONE (Matrix) DONE (INSTALL) Delete downloaded files (y/N)? y Hope this helps, Andy s-luppescu at uchicago.edu on 01/24/2001 12:02:35 PM Please respond to s-luppescu at uchicago.edu To: R Help List <r-help at stat.math.ethz.ch> cc: (bcc: Andrzej P. Jaworski/US-Corporate/3M/US) Subject: [R] update.packages() doesn''t work anymore For some reason, update.packages(), one of the greatest features of R, doesn''t work anymore (perhaps since I upgraded to 1.2.1?). It downloads the new packages, but when it tries to build them, I get this message: WARNING: ignoring environment value of R_HOME /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: No such file or directory I save the downloaded packages and then do R INSTALL <pkgname> at the command line, and it works fine. I tried setting lib=/usr/lib/R and also the R_HOME environment var, but that didn''t help. What am I doing wrong? I''m running R 1.2.1 on RedHat Linux 7 (intel). ______________________________________________________________________ Stuart Luppescu -=-=- University of Chicago $(B:MJ8$HCRF`H~$NIc(B -=-=- s-luppescu at uchicago.edu http://www.consortium-chicago.org/people/sl.html http://musuko.uchicago.edu/pubkey.asc for PGP Public Key ICQ #21172047 AIM: psycho7070 QOTD: I looked out my window, and saw Kyle Pettys'' car upside down, then I thought ''One of us is in real trouble''. -- Davey Allison, on a 150 m.p.h. crash>> Sent on 24-Jan-2001 at 11:58:45 with xfmail-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. -.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._. _._ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On 24-Jan-2001 Peter Dalgaard BSA wrote:> s-luppescu at uchicago.edu writes: > >> For some reason, update.packages(), one of the greatest features of R, >> doesn''t >> work anymore (perhaps since I upgraded to 1.2.1?). It downloads the new >> packages, but when it tries to build them, I get this message: >> >> WARNING: ignoring environment value of R_HOME >> /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: >> /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: No such file or directory >> >> I save the downloaded packages and then do R INSTALL <pkgname> at the >> command >> line, and it works fine. I tried setting lib=/usr/lib/R and also the R_HOME >> environment var, but that didn''t help. What am I doing wrong? > > What does "R RHOME" tell you?[root at musuko:~] <14:22:44> 994 ->> R RHOME /usr/lib/R> Is R_HOME set in the environment? If so, try removing it.No. R_HOME is blank. I tried setting it to /usr/lib/R but had the same results. ______________________________________________________________________ Stuart Luppescu -=-=- University of Chicago $(B:MJ8$HCRF`H~$NIc(B -=-=- s-luppescu at uchicago.edu http://www.consortium-chicago.org/people/sl.html http://musuko.uchicago.edu/pubkey.asc for PGP Public Key ICQ #21172047 AIM: psycho7070 I''ve known him as a man, as an adolescent and as a child -- sometimes on the same day.>> Sent on 24-Jan-2001 at 14:23:39 with xfmail-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On Wed, 24 Jan 2001 s-luppescu at uchicago.edu wrote:> > On 24-Jan-2001 Peter Dalgaard BSA wrote: > > s-luppescu at uchicago.edu writes: > > > >> For some reason, update.packages(), one of the greatest features of R, > >> doesn''t > >> work anymore (perhaps since I upgraded to 1.2.1?). It downloads the new > >> packages, but when it tries to build them, I get this message: > >> > >> WARNING: ignoring environment value of R_HOME > >> /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: > >> /var/tmp/R-base-root/usr/lib/R/bin/Rcmd: No such file or directory > >> > >> I save the downloaded packages and then do R INSTALL <pkgname> at the > >> command > >> line, and it works fine. I tried setting lib=/usr/lib/R and also the R_HOME > >> environment var, but that didn''t help. What am I doing wrong? > > > > What does "R RHOME" tell you? > > [root at musuko:~] <14:22:44> 994 ->> R RHOME > /usr/lib/R > > > Is R_HOME set in the environment? If so, try removing it. > > No. R_HOME is blank. I tried setting it to /usr/lib/R but had the same results.Well, it is getting /var/tmp/R-base-root/usr/lib/R/bin/ from somewhere. I think it is probably finding the wrong version of R. What does paste(file.path(R.home(), "bin", "R") give? That is what install.packages (called from update.packages) tries to run. And what does Sys.getenv("R_HOME") say?> ______________________________________________________________________ > Stuart Luppescu -=-=- University of Chicago > $(B:MJ8$HCRF`H~$NIc(B -=-=- s-luppescu at uchicago.edu > http://www.consortium-chicago.org/people/sl.html > http://musuko.uchicago.edu/pubkey.asc for PGP Public Key > ICQ #21172047 AIM: psycho7070 > I''ve known him as a man, as an adolescent and as a child -- sometimes > on the same day. > >> Sent on 24-Jan-2001 at 14:23:39 with xfmail > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html > Send "info", "help", or "[un]subscribe" > (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ >-- 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 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
install.packages want to run cmd <- paste(file.path(R.home(), "bin", "R") (which on my system is /usr/lib/R/bin/R). Unfortunately ( and this is R 1.2.1, installed from the rpm on CRAN) that shell script has /var/tmp/R-base-root/usr/lib/R hard coded as the R_Home. Here is the diff between /usr/bin/R and /usrlib/R/bin/R. ->meyer<-:/usr/lib/R/bin> diff /usr/lib/R/bin/R /usr/bin/R 4c4 < R_HOME_DIR=/var/tmp/R-base-root/usr/lib/R ---> R_HOME_DIR=/usr/lib/RA "quick" fix is to cp /usr/bin/R to /usr/lib/R/bin/R --Mike Mike Meyer, Salter Point Associates, Seattle WA -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On Wed, 24 Jan 2001, Michael M. Meyer wrote:> Brian: > I installed the 1.2.1 rpm and the scripts in /usr/lib/R/bin/R and > /usr/bin/R are different. The latter has the correct R_HOME, the former has > the one with /var/tmp/... > > Either, some postprocessing of the rpm file is broken, or the rpm > itself has a bad file in it.Ah, RPMs. Very good point, and surely the answer. Please send that to the list. -- 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 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
"Michael M. Meyer" <mikem at salter-point.com> writes:> install.packages want to run > cmd <- paste(file.path(R.home(), "bin", "R") > (which on my system is /usr/lib/R/bin/R). > > Unfortunately ( and this is R 1.2.1, installed from the rpm on CRAN) > that shell script has /var/tmp/R-base-root/usr/lib/R hard coded as the > R_Home. > > Here is the diff between /usr/bin/R and /usrlib/R/bin/R. > > ->meyer<-:/usr/lib/R/bin> diff /usr/lib/R/bin/R /usr/bin/R > 4c4 > < R_HOME_DIR=/var/tmp/R-base-root/usr/lib/R > --- > > R_HOME_DIR=/usr/lib/R > > A "quick" fix is to cp /usr/bin/R to /usr/lib/R/bin/R >Or fix the shell script (which amounts to the same). I think this happens when the RPM build installs in an alternate dir and later adjusts things for the final location. A regular install has: [pd at blueberry pd]$ R RHOME /usr/local/lib/R [pd at blueberry pd]$ cat `R RHOME`/bin/R #!/bin/sh # Shell wrapper for R executable. R_HOME_DIR=/usr/local/lib/R if test -n "${R_HOME}" && \ ... and no output from [pd at blueberry pd]$ diff `which R` `R RHOME`/bin/R We changed the use of the R_HOME environment variable recently (I forget whether it was for 1.2.0 or 1.2.1) on the premise that the startup script is really version dependent and good things couldn''t be expected to come from calling an old R script with a new R_HOME setting and that R itself ought to be able to keep track of its installation directory... The old way probably prevented a wrong R_HOME setting in /usr/lib/R/bin/R from having any effect. (Anyone with an older R installed from an RPM want to try "/usr/lib/R/bin/R RHOME"?) The fix is probably to have Martyn modify the spec file and rebuild the RPM. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /''_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Mea culpa. Updated RPMS for Red Hat 6.2 and 7.0 (Intel) which fix this problem are now up at ftp://ftp-fis.iarc.fr/pub/R and will be mirrored to CRAN shortly. Martyn. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._