[R] error in installing R packages
Eva Winter
eva at veracyte.com
Thu Aug 7 19:32:07 CEST 2008
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:ripley at stats.ox.ac.uk]
Sent: Wednesday, August 06, 2008 10:23 PM
To: Eva Winter
Cc: r-help at stat.math.ethz.ch
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]]
>
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>
--
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 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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