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Francisco Cribari

2001-Mar-07 12:56 UTC

[R] [?] update.packages() - Linux

I am running R 1.2.1 under Mandrake Linux 7.2 (installed from RPM)
and I installed a few packages using install.packages() . Now, I 
am trying to upgrade these packages using update.packages() but I 
believe I am running into some kind of error. See below. Any tips
will be greatly welcome. Thanks in advance. Francisco 

PS: update.packages() only tries to update wle from version 0.3 
to 0.4, gives me an error message at the end, and 
installed.packages() continues to list version 0.3 as the installed 
version. I ran install.packages("package-name") as root, and am 
running update.packages() as root. I must be missing something 
simple. 

-----------------------------------------------------------------

[root at edgeworth cribari]# R

R : Copyright 2001, The R Development Core Team
Version 1.2.1  (2001-01-15)

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.

Type `demo()' for some demos, `help()' for on-line help, or
`help.start()' for a HTML browser interface to help.
Type `q()' to quit R.
> installed.packages()      Package      LibPath              Version  Priority Bundle Depends
 [1,] "base"       "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [2,] "ctest"      "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   ""
 [3,] "eda"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [4,] "ineq"       "/usr/lib/R/library" "0.1-2" 
"NA"     "NA"   "NA"
 [5,] "KernSmooth" "/usr/lib/R/library" "2.22-4"
"NA"     "NA"   "NA"
 [6,] "lmtest"     "/usr/lib/R/library" "0.1-9" 
"NA"     "NA"   ""
 [7,] "lqs"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [8,] "modreg"     "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [9,] "mva"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[10,] "nls"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[11,] "quantreg"   "/usr/lib/R/library" "3.01-1"
"NA"     "NA"   "NA"
[12,] "splines"    "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[13,] "stepfun"    "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[14,] "tcltk"      "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[15,] "ts"         "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[16,] "wle"        "/usr/lib/R/library" "0.3"   
"NA"     "NA"   "NA"   >update.packages()--10:36:29--  http://cran.r-project.org:80/src/contrib/PACKAGES
           => `/tmp/fileR5148S327b23c6'
Connecting to cran.r-project.org:80... connected!
HTTP request sent, awaiting response... 200 OK
Length: 38,275 [text/plain]

    0K .......... .......... .......... .......              100%   0:00 9.06K

10:36:42 (8.85 KB/s) - `/tmp/fileR5148S327b23c6' saved [38275/38275]

wle :
 Version 0.3 in /usr/lib/R/library 
 Version 0.4 on CRAN
Update (y/N)?  y
--10:37:38--  http://cran.r-project.org:80/src/contrib/wle_0.4.tar.gz
           => `/tmp/RinstdirR5148S643c9869/wle_0.4.tar.gz'
Connecting to cran.r-project.org:80... connected!
HTTP request sent, awaiting response... 200 OK
Length: 131,087 [application/x-tar]

    0K .......... .......... .......... .......... .......... 39%   1:21  978B
   50K .......... .......... .......... .......... .......... 78%   0:18 1.56K
  100K .......... .......... ........                        100%   0:00  869B

10:39:37 (1.08 KB/s) - `/tmp/RinstdirR5148S643c9869/wle_0.4.tar.gz' saved
[131087/131087]

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

Delete downloaded files (y/N)? y

Warning message: 
Installation of package wle had non-zero exit status in:
install.packages(update[, "Package"], instlib, contriburl =
contriburl,  >installed.packages() 
      Package      LibPath              Version  Priority Bundle Depends
 [1,] "base"       "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [2,] "ctest"      "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   ""
 [3,] "eda"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [4,] "ineq"       "/usr/lib/R/library" "0.1-2" 
"NA"     "NA"   "NA"
 [5,] "KernSmooth" "/usr/lib/R/library" "2.22-4"
"NA"     "NA"   "NA"
 [6,] "lmtest"     "/usr/lib/R/library" "0.1-9" 
"NA"     "NA"   ""
 [7,] "lqs"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [8,] "modreg"     "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
 [9,] "mva"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[10,] "nls"        "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[11,] "quantreg"   "/usr/lib/R/library" "3.01-1"
"NA"     "NA"   "NA"
[12,] "splines"    "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[13,] "stepfun"    "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[14,] "tcltk"      "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[15,] "ts"         "/usr/lib/R/library" "1.2.1" 
"base"   "NA"   "NA"
[16,] "wle"        "/usr/lib/R/library" "0.3"   
"NA"     "NA"   "NA"


-- 
   _                                                         _  
  (o-               Francisco Cribari-Neto                  -o)
  //\  Dept. de Estatistica, Univ. Federal de Pernambuco    /\\  
 .v_/_....................................................._\_v.
/      Phone: (+55-81) 3271-8420  Fax: (+55-81) 3271-8422       \
:      Email: cribari at de.ufpe.br  Web: www.de.ufpe.br/~cribari  :
:                                                               : 
:      Linux: more Unix than Unix.        http://www.linux.org  :
\.............................................................../


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Prof Brian Ripley

2001-Mar-07 15:10 UTC

head link

[R] [?] update.packages() - Linux

> Date: Wed, 7 Mar 2001 09:56:17 -0300 (EST)
> From: Francisco Cribari <cribari at de.ufpe.br>
> To: r-help at stat.math.ethz.ch
> Subject: [R] [?] update.packages() - Linux
> 
> I am running R 1.2.1 under Mandrake Linux 7.2 (installed from RPM)
> and I installed a few packages using install.packages() . Now, I 
> am trying to upgrade these packages using update.packages() but I 
> believe I am running into some kind of error. See below. Any tips
> will be greatly welcome. Thanks in advance. Francisco 
Mike Meyer solved this on 24 Jan:

   Date: Wed, 24 Jan 2001 13:48:53 -0800
   From: "Michael M. Meyer" <mikem at salter-point.com>
   
   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


Follow the thread in the R-help archives if you want to know more.

-- 
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

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