[R] Problem installing packages in newer versions of R
Dear all, I was wandering what could be wrong with my system (regularly updated Fedora core 8) so that installing packages does not succeed with almost every package. I follow the procedure specified in the help file R-admin section 6.3. This is not a feature new to the current version but happened (to me) in the previous version as well. Additionally R-help html pages try to follow wrong links for the packages that manage to get thorough install.packages() (e.g. RColorBrewer). Should I specify a different lib.loc during install.packages()? My base packages currently reside in /usr/lib/R/library, however, html links for the mentioned contributed package RColorBrewer try to follow a non-existent /usr/share/doc/library/RColorBrewer/html/00Index.html. Why? What should I set to make my default library location (for html links as well) /usr/lib/R/library and default R location /usr/lib/R? Are these two problems connected or the are not? I have even built the rpm from src.rpm myself but with no change. Below you may find the (error) output from installing the akima package. It might give a clue. Thanks for your help. Miha - install.packages(akima,repos=http://cran.r-project.org,depend=T) Warning in install.packages(akima, repos = http://cran.r-project.org;, : argument 'lib' is missing: using '/usr/lib/R/library' trying URL 'http://cran.r-project.org/src/contrib/akima_0.5-1.tar.gz' Content type 'application/x-gzip' length 148838 bytes (145 Kb) opened URL == downloaded 145 Kb * Installing *source* package 'akima' ... ** libs gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima433.f -o akima433.o In file akima433.f:49 IF(X(I-1)-X(I)) 11,95,96 1 Warning: Obsolete: arithmetic IF statement at (1) In file akima433.f:38 10 L0=L 1 Warning: Label 1 at (1) defined but not used In file akima433.f:56 20 IF(LM2.EQ.0) GO TO 27 1 Warning: Label 20 at (1) defined but not used In file akima433.f:63 22 IMX=I 1 Warning: Label 22 at (1) defined but not used In file akima433.f:79 40 J=I 1 Warning: Label 40 at (1) defined but not used In file akima433.f:166 99 ERR = 10 1 Warning: Label 99 at (1) defined but not used gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima697.f -o akima697.o In file akima697.f:88 10 IF (ND.LE.1) GO TO 90 1 Warning: Label 10 at (1) defined but not used In file akima697.f:97 20 NP0=MAX(3,NP) 1 Warning: Label 20 at (1) defined but not used In file akima697.f:103 30 DO 39 II=1,NI 1 Warning: Label 30 at (1) defined but not used In file akima697.f:398 99 ERR=10 1 Warning: Label 99 at (1) defined but not used gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima.new.f -o akima.new.o akima.new.f: In function ‘sdplnl’: akima.new.f:1904: warning: ‘zii1’ may be used uninitialized in this function akima.new.f:1903: warning: ‘y0’ may be used uninitialized in this function akima.new.f:1903: warning: ‘wt2’ may be used uninitialized in this function akima.new.f:1903: warning: ‘p50’ may be used uninitialized in this function akima.new.f:1903: warning: ‘p41’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p40’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p31’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p32’ may be used uninitialized in this function akima.new.f:1903: warning: ‘x0’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p22’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p21’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p23’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p13’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p14’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p12’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p20’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p10’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p04’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p02’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p03’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p05’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p11’ may be used
Re: [R] Problem installing packages in newer versions of R
Thanks for your help Hadley and Peter. Your suggestions solved the question of installing new packages. But what can be done to get rid of the other mentioned problem in html help files. I am repeating what the problem is. After installation of new packages R-html help files try to follow non-existent links for new packages. The help files for akima, for instance, reside in /usr/lib/R/library/akima/html/00index.html, the link however leads to this address /usr/share/doc/library/akima/html/00index.html. I know it is a minor problem but I am used to query html help a lot and it bothers. Thanks again Miha --- On Thu, 18/9/08, hadley wickham [EMAIL PROTECTED] wrote: From: hadley wickham [EMAIL PROTECTED] Subject: Re: [R] Problem installing packages in newer versions of R To: [EMAIL PROTECTED] Cc: r-help@r-project.org Date: Thursday, 18 September, 2008, 5:12 PM Hi Miha, One tip for diagnosing build problems is to ignore all warnings and look for the first error. In your case it's: init.c:2:15: error: R.h: No such file or directory init.c:3:24: error: Rinternals.h: No such file or directory Which possibly suggests that you don't have the necessary headers. One common reason for this is that you haven't installed the development rpm for R which contains all the header files to compile stuff - you probably just have the user package which allows you to use R. Hadley On Thu, Sep 18, 2008 at 10:04 AM, Miha Staut [EMAIL PROTECTED] wrote: Dear all, I was wandering what could be wrong with my system (regularly updated Fedora core 8) so that installing packages does not succeed with almost every package. I follow the procedure specified in the help file R-admin section 6.3. This is not a feature new to the current version but happened (to me) in the previous version as well. Additionally R-help html pages try to follow wrong links for the packages that manage to get thorough install.packages() (e.g. RColorBrewer). Should I specify a different lib.loc during install.packages()? My base packages currently reside in /usr/lib/R/library, however, html links for the mentioned contributed package RColorBrewer try to follow a non-existent /usr/share/doc/library/RColorBrewer/html/00Index.html. Why? What should I set to make my default library location (for html links as well) /usr/lib/R/library and default R location /usr/lib/R? Are these two problems connected or the are not? I have even built the rpm from src.rpm myself but with no change. Below you may find the (error) output from installing the akima package. It might give a clue. Thanks for your help. Miha __ R-help@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.
[R] Help with installing add-on packages
Dear R users. Recently I wanted to update my R distribution to the current one (R-2.7.1). I am running a Fedora core 8 distirbution. The installation went fine, but when I tried to add some additional packages the majority made an exit with an error. Only a few least demanding (e.g. RColorBrewer) managed to get through the installation process. What happened between the versions 2.6.x and 2.7.x to impede the installation of add-on packages that previously went smooth? Thank you for your suggestions and best regards. Miha Example: install.packages(akima,repos=http://cran.r-project.org,depend=T) * Installing to library '/usr/lib/R/library' * Installing *source* package 'akima' ... ** libs gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima433.f -o akima433.o In file akima433.f:49 IF(X(I-1)-X(I)) 11,95,96 1 Warning: Obsolete: arithmetic IF statement at (1) In file akima433.f:38 10 L0=L 1 Warning: Label 1 at (1) defined but not used In file akima433.f:56 20 IF(LM2.EQ.0) GO TO 27 1 Warning: Label 20 at (1) defined but not used In file akima433.f:63 22 IMX=I 1 Warning: Label 22 at (1) defined but not used In file akima433.f:79 40 J=I 1 Warning: Label 40 at (1) defined but not used In file akima433.f:166 99 ERR = 10 1 Warning: Label 99 at (1) defined but not used gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima697.f -o akima697.o In file akima697.f:88 10 IF (ND.LE.1) GO TO 90 1 Warning: Label 10 at (1) defined but not used In file akima697.f:97 20 NP0=MAX(3,NP) 1 Warning: Label 20 at (1) defined but not used In file akima697.f:103 30 DO 39 II=1,NI 1 Warning: Label 30 at (1) defined but not used In file akima697.f:398 99 ERR=10 1 Warning: Label 99 at (1) defined but not used gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima.new.f -o akima.new.o akima.new.f: In function ‘sdplnl’: akima.new.f:1904: warning: ‘zii1’ may be used uninitialized in this function akima.new.f:1903: warning: ‘y0’ may be used uninitialized in this function akima.new.f:1903: warning: ‘wt2’ may be used uninitialized in this function akima.new.f:1903: warning: ‘p50’ may be used uninitialized in this function akima.new.f:1903: warning: ‘p41’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p40’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p31’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p32’ may be used uninitialized in this function akima.new.f:1903: warning: ‘x0’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p22’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p21’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p23’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p13’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p14’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p12’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p20’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p10’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p04’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p02’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p03’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p05’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p11’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p30’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p00’ may be used uninitialized in this function akima.new.f:1900: warning: ‘cp’ may be used uninitialized in this function akima.new.f:1899: warning: ‘bp’ may be used uninitialized in this function akima.new.f:1898: warning: ‘ap’ may be used uninitialized in this
[R] Help with installing add-on packages
Dear R users. Recently I wanted to update my R distribution to the current one (R-2.7.1). I am running a Fedora core 8 distirbution. The installation went fine, but when I tried to add some additional packages the majority made an exit with an error. Only a few least demanding (e.g. RColorBrewer) managed to get through the installation process. What happened between the versions 2.6.x and 2.7.x to impede the installation of add-on packages that previously went smooth? Thank you for your suggestions and best regards. Miha Example: install.packages(akima,repos=http://cran.r-project.org,depend=T) * Installing to library '/usr/lib/R/library' * Installing *source* package 'akima' ... ** libs gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima433.f -o akima433.o In file akima433.f:49 IF(X(I-1)-X(I)) 11,95,96 1 Warning: Obsolete: arithmetic IF statement at (1) In file akima433.f:38 10 L0=L 1 Warning: Label 1 at (1) defined but not used In file akima433.f:56 20 IF(LM2.EQ.0) GO TO 27 1 Warning: Label 20 at (1) defined but not used In file akima433.f:63 22 IMX=I 1 Warning: Label 22 at (1) defined but not used In file akima433.f:79 40 J=I 1 Warning: Label 40 at (1) defined but not used In file akima433.f:166 99 ERR = 10 1 Warning: Label 99 at (1) defined but not used gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima697.f -o akima697.o In file akima697.f:88 10 IF (ND.LE.1) GO TO 90 1 Warning: Label 10 at (1) defined but not used In file akima697.f:97 20 NP0=MAX(3,NP) 1 Warning: Label 20 at (1) defined but not used In file akima697.f:103 30 DO 39 II=1,NI 1 Warning: Label 30 at (1) defined but not used In file akima697.f:398 99 ERR=10 1 Warning: Label 99 at (1) defined but not used gfortran -m32 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c akima.new.f -o akima.new.o akima.new.f: In function ‘sdplnl’: akima.new.f:1904: warning: ‘zii1’ may be used uninitialized in this function akima.new.f:1903: warning: ‘y0’ may be used uninitialized in this function akima.new.f:1903: warning: ‘wt2’ may be used uninitialized in this function akima.new.f:1903: warning: ‘p50’ may be used uninitialized in this function akima.new.f:1903: warning: ‘p41’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p40’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p31’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p32’ may be used uninitialized in this function akima.new.f:1903: warning: ‘x0’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p22’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p21’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p23’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p13’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p14’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p12’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p20’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p10’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p04’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p02’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p03’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p05’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p11’ may be used uninitialized in this function akima.new.f:1902: warning: ‘p30’ may be used uninitialized in this function akima.new.f:1901: warning: ‘p00’ may be used uninitialized in this function akima.new.f:1900: warning: ‘cp’ may be used uninitialized in this function akima.new.f:1899: warning: ‘bp’ may be used uninitialized in this function akima.new.f:1898: warning: ‘ap’ may be used uninitialized in this function
[R] Cluster analysis with numeric and categorical variables
Dear all, I would like to perform a clustering analysis on a data frame with two coordinate variables (X and Y) and a categorical variable where only a != b can be established. As far as I understood classification analyses, they are not an option as they partition the training set only in k classes of the test set. By searching through the book Modern Applied Statistics with S I did not find a satisfactory solution. I will be grateful for any suggestions. Best regards Miha __ can.html __ R-help@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.
