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
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