[R] Package installed, functional but not available
Hello, when I run packageStatus(), I get the following results: packageStatus() Number of installed packages: ok upgrade unavailable /home/fernando/my_library 38 0 1 /usr/local/lib/R/library 28 0 0 Number of available packages (each package/bundle counted only once): installed not installed http://cran-r.c3sl.ufpr.br/src/contrib51 957 i.e., there is an unavailable package in my personal library. With, summary(packageStatus()) I see that the unavailable package is one that I have done and installed via R CMD INSTALL. Although it says it is unavailable, I can load the package with library() and use its functions in the usual way. There is no problem at all here since I can use the functions. I was just curious about what really means this unavailable classification. My guess is that this a package that is not on CRAN (?). This is version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R Thanks for any explanations, --- Fernando Mayer Fisheries Study Group Technology, Earth and Ocean Sciences Center University of Vale do Itajaí Itajaí - SC - Brazil __ R-help@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.
Re: [R] Off topic:Spam on R-help increase?
Not in the past 2 days, but only today I've received already more than 40 spams from R-help and R-sig-* too. Rarely I received a spam from these lists... Fernando Mayer. Bert Gunter escreveu: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? Feel free to reply privately. Thanks. Bert Gunter Genentech Nonclinical Statistics South San Francisco, CA 94404 650-467-7374 __ R-help@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. __ R-help@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.
Re: [R] R --gui=GNOME problem
I had the same problem, and I fixed following Dirk Eddelbuettel's suggestion on R-sig-Debian some time ago: install also the package gnomeGUI to have it working. HTH, --- Fernando Mayer Grupo de Estudos Pesqueiros - GEP Centro de Ciências Tecnológicas, da Terra e do Mar - CTTMar Universidade do Vale do Itajaí - UNIVALI Itajaí - SC - Brasil pacocuacco escreveu: I've installed GNU R statistical comupting language and environment 2.2.1-2 by Synaptic (on Ubunti Linux 6.06 Dapper Drake). I've installed also r-gnome to have a GUI. I can't start my GUI. Why R --gui=GNOME don't start? It cannot find rgnome. R --gui=tk command instead is good. What's the best GUI for R? How can I start my GUI? Thanks Paco __ R-help@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 __ R-help@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
Re: [R] putting text in the corner
You can get the x and y position of any place of an open graphic device with the mouse cursor, using the function locator(), and even assing this values to an object, as in: xy-locator() You will have a list with x and y positions. Then you can use: text(xy$x,xy$y,...) See ?locator. HTH, Fernando Mayer. Thomas Steiner escreveu: I want to write some text in a corner of my plot. Is it possible to get the xlim and ylim of an open window? Or is there anything similar like legend(x=bottomright, inset=0.01,legend=...) for text(x=1,y=2, test) Thomas __ R-help@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 [[alternative HTML version deleted]] __ R-help@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
Re: [R] Can¢t find X11 font when tryi ng to produce graph
Also check if you have installed in your Ubuntu-Breezy: xfonts-utils xfonts-base xfonts-75dpi xfonts-100dpi xfonts-scalable If you don't have one of this, try to install it and see if now works. Hope this helps, Fernando Mayer. Dominik Heier escreveu: I don't think this is a R internal problem. It seems that some fonts are missing that were not included in your X11 installation. However, you could upgrade to R 2.2.1 and hope that the problem disappears. Do so by adding: deb http://cran.R-project.org/bin/linux/debian stable/ to your /etc/apt/sources.list (or via synaptic) and reinstall/update R. On my ubuntu-breezy system (no laptop, amd-k7) I never had any problems with this configuration. Hope this helps Dominik Am Dienstag, den 24.01.2006, 14:53 +0100 schrieb Petar Milin: I am using R 2.1.1 on i486-pc-gnu-linux (Ubuntu Breezy). Recently, I bought new laptop HP nx8220 and installed Breezy with a few problems starting X-Windows. Nevertheless, I followed some instruction, managed to start X, and added R from the Ubuntu's repositories. When I try to produce any graph (like plot, bwplot etc.), I receive an error message: can't find X11 font Error in X11( unable to start device X11 I wonder if it is related to the problem that Ubuntu complained of, or it is just something internal to R. In any case, I would really appreciate help on that matter. Sincerely, Petar Milin __ R-help@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 __ R-help@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 [[alternative HTML version deleted]] __ R-help@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
Re: [R] Error in make check-all
Dear Peter Dalgaard, first, sorry for my delay to this reply, but I only have acces to this machine in the morning (consider also the time it takes to run make and make check)... It seems that the problem was really with some missing -devel packages. I followed your suggestions and installed libjpeg-devel, tk-devel and tcl-devel. The readline-devel and xorg-x11-devel packages were already installed. After this, I also re-built R, now as 'normal' user to my home folder (/home/fernando/programs/R-2.1.1). So I re-run again make check, make check-devel and make check-all. Everything seems OK now. No more those warnings in tcltk package and in any other. Now going to installation... Thank you very much for your (and Prof Brian Ripley) help! Fernando Mayer. Peter Dalgaard escreveu: Fernando Mayer [EMAIL PROTECTED] writes: Dear Prof. Ripley, that was exactly what i did. Should i login on the system as root, instead of login as user and became root via console? What should i do to have X11 usable? I don't actually think that this is the problem. You shouldn't generally trust me rather than Brian, but I'm sitting at a SUSE 9.3 system, and he's not... If I su - to root, I can happily run xterm etc. from the root shell with display on the console, and also run make check on the current r-devel. So go look for missing RPM packages. That said, it is not generally a good idea to build as root. I prefer to build things as myself and only do the final install step as root if necessary. -pd (PS: I had a powercut when I was either 99.99% or 100.01% done with writing this before. Apologies if it went out twice...) Thanks, Fernando Mayer. Prof Brian Ripley escreveu: This is what happens if you don't have a usable X11 display. Did you perhaps use a root account on a console owned by a normal user? On Tue, 27 Sep 2005, Fernando Mayer wrote: Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library
[R] Error in make check-all
Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution * checking Rd \usage sections ... OK * checking DVI version of manual ... OK [end log file] The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu [SuSE 9.3] system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R [[alternative HTML version deleted]] __ R-help@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
Re: [R] Error in make check-all
Dear Prof. Ripley, that was exactly what i did. Should i login on the system as root, instead of login as user and became root via console? What should i do to have X11 usable? Thanks, Fernando Mayer. Prof Brian Ripley escreveu: This is what happens if you don't have a usable X11 display. Did you perhaps use a root account on a console owned by a normal user? On Tue, 27 Sep 2005, Fernando Mayer wrote: Dear R-users, i'm a very newbie in linux, but decided to build R from source. Following the R Installation and Administration manual, i did this: ./configure --enable-R-shlib # this option is here because i intend to build the GNOME console after... make make check no problems in make check, but: make check-devel #and also make check-all indicated some WARNINGs in the log file: /usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck Right below is the content of this log file (I translated some words): [start log file] * using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck' * using R version 2.1.1, 2005-06-20 * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking S3 generic/method consistency ... WARNING Erro: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution Error: .First.lib failed for 'tcltk' Call sequence: 2: stop(gettextf(.First.lib failed for '%s', libraryPkgName(package)), domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Interrupted execution * checking Rd \usage sections ... OK * checking DVI version of manual ... OK [end log file] The problem is in the tcltk package. I have searched in the archives, but didin't find anything similar to this problem (maybe there is, but i was not able to identify it). I really don't know what all the warnings means. What i need to know is what am i missing, and if there is something i can fix it. Also, are there any problems if i continue the installation without fix something? P.S.: actually R is running already from where it was buit, but i want to install it. So i want to avoid future problems, if this warnings really make some. Any help is appreciated. Thanks! Fernando Mayer. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu [SuSE 9.3] system i686, linux-gnu status major2 minor1.1 year 2005 month06 day 20 language R [[alternative HTML version deleted]] __ R-help@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
