Thanks for the tips. The R installation is pre-existing, I will check to see what's happening.
Regards, -e -----Original Message----- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Wednesday, August 06, 2008 10:23 PM To: Eva Winter Cc: [EMAIL PROTECTED] Subject: Re: [R] error in installing R packages Did you install a binary version of R and forget to install the corresponding -devel version? E.g. for Fedora your need both the R and R-devel RPMs to install packages. Doing this shows a lack of understanding of R (which is not a library and needs those files as part of the basic functioning of R), so a bug report on a distribution which did so would be appropriate. On Wed, 6 Aug 2008, Eva Winter wrote: > Hello, > > > > I am trying to install R packages under linux, some of the packages can > not be installed and I got the following errors, could anybody give me > suggestion on where the problem is and how to fix them? Thanks -e > > > >> .libPaths() > > [1] "/usr/lib64/R/library" > > [2] "/usr/share/R/library" > > [3] "/home/ewinter/R/x86_64-redhat-linux-gnu-library/2.7" > >> install.packages("e1071", lib="/usr/share/R/library", dependencies=T) > > also installing the dependencies ?mlbench?, ?randomForest? > > > > trying URL 'http://cran.stat.ucla.edu/src/contrib/mlbench_1.1-4.tar.gz' > > Content type 'application/x-tar' length 1192839 bytes (1.1 Mb) > > opened URL > > ================================================== > > downloaded 1.1 Mb > > > > trying URL > 'http://cran.stat.ucla.edu/src/contrib/randomForest_4.5-25.tar.gz' > > Content type 'application/x-tar' length 70212 bytes (68 Kb) > > opened URL > > ================================================== > > downloaded 68 Kb > > > > trying URL 'http://cran.stat.ucla.edu/src/contrib/e1071_1.5-18.tar.gz' > > Content type 'application/x-tar' length 311174 bytes (303 Kb) > > opened URL > > ================================================== > > downloaded 303 Kb > > > > * Installing *source* package 'mlbench' ... > > ** libs > > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 > -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c waveform.c -o > waveform.o > > waveform.c:17:26: error: R_ext/Random.h: No such file or directory > > waveform.c: In function ?waveform?: > > waveform.c:35: warning: implicit declaration of function ?GetRNGstate? > > waveform.c:38: warning: implicit declaration of function ?PutRNGstate? > > waveform.c: In function ?execute?: > > waveform.c:100: warning: implicit declaration of function ?unif_rand? > > waveform.c:115: warning: implicit declaration of function ?norm_rand? > > make: *** [waveform.o] Error 1 > > ERROR: compilation failed for package 'mlbench' > > ** Removing '/usr/share/R/library/mlbench' > > * Installing *source* package 'randomForest' ... > > ** libs > > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 > -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 > -mtune=generic -c classTree.c -o classTree.o > > classTree.c:15:15: error: R.h: No such file or directory > > classTree.c:16:19: error: Rmath.h: No such file or directory > > In file included from classTree.c:17: > > rf.h:95: error: ?F77_NAME? declared as function returning a function > > rf.h:95: warning: parameter names (without types) in function > declaration > > classTree.c:292: error: ?F77_NAME? declared as function returning a > function > > classTree.c: In function ?F77_NAME?: > > classTree.c:292: warning: type of ?catmax? defaults to ?int? > > classTree.c:302: warning: implicit declaration of function ?Calloc? > > classTree.c:302: error: ?nclass? undeclared (first use in this function) > > classTree.c:302: error: (Each undeclared identifier is reported only > once > > classTree.c:302: error: for each function it appears in.) > > classTree.c:302: error: expected expression before ?double? > > classTree.c:302: warning: cast to pointer from integer of different size > > classTree.c:303: error: ?nhit? undeclared (first use in this function) > > classTree.c:304: error: ?lcat? undeclared (first use in this function) > > classTree.c:304: error: ?ncmax? undeclared (first use in this function) > > classTree.c:305: error: ?ncsplit? undeclared (first use in this > function) > > classTree.c:305: warning: implicit declaration of function ?pow? > > classTree.c:305: warning: incompatible implicit declaration of built-in > function ?pow? > > classTree.c:313: warning: implicit declaration of function ?unif_rand? > > classTree.c:321: error: ?tclasscat? undeclared (first use in this > function) > > classTree.c:332: error: ?parentDen? undeclared (first use in this > function) > > classTree.c:335: error: ?tclasspop? undeclared (first use in this > function) > > classTree.c:339: error: ?critmax? undeclared (first use in this > function) > > classTree.c:342: error: ?ncatsp? undeclared (first use in this function) > > classTree.c:345: warning: implicit declaration of function ?Free? > > classTree.c: At top level: > > classTree.c:353: error: ?F77_NAME? declared as function returning a > function > > classTree.c:351: error: redefinition of ?F77_NAME? > > classTree.c:292: error: previous definition of ?F77_NAME? was here > > classTree.c: In function ?F77_NAME?: > > classTree.c:353: warning: type of ?catmaxb? defaults to ?int? > > classTree.c:360: error: ?nhit? undeclared (first use in this function) > > classTree.c:361: error: ?nCat? undeclared (first use in this function) > > classTree.c:362: error: ?catCount? undeclared (first use in this > function) > > classTree.c:363: error: ?tclasscat? undeclared (first use in this > function) > > classTree.c:363: error: ?nclass? undeclared (first use in this function) > > classTree.c:366: warning: implicit declaration of function ?R_qsort_I? > > classTree.c:369: error: ?classCount? undeclared (first use in this > function) > > classTree.c:371: error: ?totalWt? undeclared (first use in this > function) > > classTree.c:388: error: ?critmax? undeclared (first use in this > function) > > classTree.c:403: error: ?nbest? undeclared (first use in this function) > > classTree.c: In function ?predictClassTree?: > > classTree.c:418: error: expected expression before ?int? > > classTree.c:418: warning: cast to pointer from integer of different size > > make: *** [classTree.o] Error 1 > > ERROR: compilation failed for package 'randomForest' > > ** Removing '/usr/share/R/library/randomForest' > > * Installing *source* package 'e1071' ... > > checking for C++ compiler default output file name... a.out > > checking whether the C++ compiler works... yes > > checking whether we are cross compiling... no > > checking for suffix of executables... > > checking for suffix of object files... o > > checking whether we are using the GNU C++ compiler... yes > > checking whether g++ -m64 accepts -g... yes > > ** libs > > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 > -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 > -mtune=generic -c cmeans.c -o cmeans.o > > cmeans.c:5:15: error: R.h: No such file or directory > > cmeans.c: In function ?cmeans_setup?: > > cmeans.c:20: warning: implicit declaration of function ?R_alloc? > > cmeans.c:20: warning: cast to pointer from integer of different size > > cmeans.c:23: warning: cast to pointer from integer of different size > > cmeans.c:24: warning: cast to pointer from integer of different size > > cmeans.c:25: warning: cast to pointer from integer of different size > > cmeans.c:26: warning: cast to pointer from integer of different size > > cmeans.c: In function ?cmeans_weighted_median?: > > cmeans.c:66: warning: implicit declaration of function > ?rsort_with_index? > > cmeans.c:79: error: ?R_PosInf? undeclared (first use in this function) > > cmeans.c:79: error: (Each undeclared identifier is reported only once > > cmeans.c:79: error: for each function it appears in.) > > cmeans.c: In function ?cmeans?: > > cmeans.c:253: warning: implicit declaration of function ?Rprintf? > > make: *** [cmeans.o] Error 1 > > chmod: cannot access `/usr/share/R/library/e1071/libs/*': No such file > or directory > > ERROR: compilation failed for package 'e1071' > > ** Removing '/usr/share/R/library/e1071' > > > > The downloaded packages are in > > /tmp/RtmpZ0Gndg/downloaded_packages > > Warning messages: > > 1: In install.packages("e1071", lib = "/usr/share/R/library", > dependencies = T) : > > installation of package 'mlbench' had non-zero exit status > > 2: In install.packages("e1071", lib = "/usr/share/R/library", > dependencies = T) : > > installation of package 'randomForest' had non-zero exit status > > 3: In install.packages("e1071", lib = "/usr/share/R/library", > dependencies = T) : > > installation of package 'e1071' had non-zero exit status > > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > -- Brian D. Ripley, [EMAIL PROTECTED] 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 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ 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.
