[R] error in installing R packages 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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