Rstem and sentiment package installation issue - r

It seems without Rstem and sentiment packages twitter sentiment analysis
is difficult.
I am trying this Rstem and sentiment packages installation using the tar.gz file
(as no windows binary available in omegahat or in the github of Timothy P. Jurka)
but it gives an error:
installation of package 'Rstem' had non-zero exit status
I tried even command prompt. That gives below error. Any clue how to solve it ? my system is windows 7, R 2.15, Rstudio.
D:\R Projects>R CMD INSTALL Rstem_0.4-1.tar.gz
* installing to library 'D:/R-Econometrics/R-2.15.1/library'
* installing *source* package 'Rstem' ...
** libs
*** arch - i386
D:/R-Econometrics/R-2.15.1/etc/i386/Makeconf:194: warning: overriding recipe for
target `.m.o'
D:/R-Econometrics/R-2.15.1/etc/i386/Makeconf:187: warning: ignoring old recipe f
or target `.m.o'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c api.c -o api.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c danish_stem.c -o danish_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c dutch_stem.c -o dutch_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c english_stem.c -o english_stem.o
english_stem.c: In function 'r_prelude':
english_stem.c:376:5: warning: label 'lab1' defined but not used
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c finnish_stem.c -o finnish_stem.o
finnish_stem.c: In function 'r_case':
finnish_stem.c:448:21: warning: unused variable 'm'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c french_stem.c -o french_stem.o
french_stem.c: In function 'french_stem':
french_stem.c:951:25: warning: unused variable 'm'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c german_stem.c -o german_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c mytest.c -o mytest.o
mytest.c: In function 'S_stemWords':
mytest.c:76:3: warning: pointer targets in passing argument 1 of 'Rf_mkChar' dif
fer in signedness
D:/R-Econometrics/R-2.15.1/include/Rinternals.h:628:6: note: expected 'const cha
r *' but argument is of type 'symbol *'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c norwegian_stem.c -o norwegian_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c portuguese_stem.c -o portuguese_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c russian_stem.c -o russian_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c spanish_stem.c -o spanish_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c swedish_stem.c -o swedish_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
process_begin: CreateProcess(NULL, basename Rstem.dll .dll, ...) failed.
process_begin: CreateProcess(NULL, basename Rstem.dll .dll, ...) failed.
process_begin: CreateProcess(NULL, basename Rstem.dll .dll, ...) failed.
"zapi.o danish_stem.o dutch_stem.o english_stem.o finnish_stem.o french_stem.o g
erman_stem.o mytest.o norwegian_stem.o portuguese_stem.o russian_stem.o spanish_
stem.o swedish_stem.o utilities.o" was unexpected at this time.
make: *** [Rstem.dll] Error 255
ERROR: compilation failed for package 'Rstem'
* removing 'D:/R-Econometrics/R-2.15.1/library/Rstem'

Related

R throwing an error when trying to compile packages R 4.2.1 RTools 4.2

When trying to download and compile a package, I get every time the following error message:
installiere Quellpaket ‘collections’
trying URL 'https://cran.rstudio.com/src/contrib/collections_0.3.6.tar.gz'
Content type 'application/x-gzip' length 93546 bytes (91 KB)
downloaded 91 KB
* installing *source* package 'collections' ...
** Paket 'collections' erfolgreich entpackt und MD5 Summen überprüft
** using staged installation
** libs
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tommyds/tommy.c -o tommyds/tommy.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c collections.c -o collections.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c deque.c -o deque.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c dict.c -o dict.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c priority_queue.c -o priority_queue.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c queue.c -o queue.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stack.c -o stack.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xxh.c -o xxh.o
gcc -I"/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
gcc -shared -s -static-libgcc -o collections.dll tmp.def tommyds/tommy.o collections.o deque.o dict.o priority_queue.o queue.o stack.o xxh.o utils.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -L/bin/x64 -lR
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: cannot find -lR
collect2.exe: error: ld returned 1 exit status
keine DLL erzeugt
ERROR: compilation failed for package 'collections'
* removing 'C:/Users/kantorov/AppData/Local/R/win-library/4.2/collections'
* restoring previous 'C:/Users/kantorov/AppData/Local/R/win-library/4.2/collections'
Warning in install.packages :
Installation des Pakets ‘collections’ hatte Exit-Status ungleich 0
Die heruntergeladenen Quellpakete sind in
‘C:\Users\kantorov\AppData\Local\Temp\RtmpOIOfZe\downloaded_packages’
>
I am using RTools 4.2 and Windows 11. Is there anything I need to take care of for compilation to work properly?

Unable to Install openxlsx library in R

I have been trying to install "openxlsx" library in R. I have R 3.4.0 and tried installing "openxlsx" from cran and from package archive (local folder) as well but none of them let me install this package. Below is the log message. Can someone please help.
> install.packages("C:/Users/rgowriga/Downloads/openxlsx_4.0.17.tar.gz", repos = NULL, type = "source")
'\\...\rgowriga$\Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'openxlsx' ...
** package 'openxlsx' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c helper_functions.cpp -o helper_functions.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c load_workbook.cpp -o load_workbook.o
C:/PF/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c openxlsx_init.c -o openxlsx_init.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c read_workbook.cpp -o read_workbook.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_data.cpp -o write_data.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file.cpp -o write_file.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file_2.cpp -o write_file_2.o
C:/PF/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o openxlsx.dll tmp.def RcppExports.o helper_functions.o load_workbook.o openxlsx_init.o read_workbook.o write_data.o write_file.o write_file_2.o -Ld:/Compiler/gcc-4.9.3/local330/lib/i386 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-34~1.0/bin/i386 -lR
installing to C:/Program Files/R/R-3.4.0/library/openxlsx/libs/i386
*** arch - x64
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c helper_functions.cpp -o helper_functions.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c load_workbook.cpp -o load_workbook.o
C:/PF/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -std=gnu99 -mtune=core2 -c openxlsx_init.c -o openxlsx_init.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c read_workbook.cpp -o read_workbook.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_data.cpp -o write_data.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file.cpp -o write_file.o
C:/PF/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c write_file_2.cpp -o write_file_2.o
C:/PF/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o openxlsx.dll tmp.def RcppExports.o helper_functions.o load_workbook.o openxlsx_init.o read_workbook.o write_data.o write_file.o write_file_2.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-34~1.0/bin/x64 -lR
C:/PROGRA~1/R/R-34~1.0/bin/x64/R.dll: file not recognized: File format not recognized
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'openxlsx'
* removing 'C:/Program Files/R/R-3.4.0/library/openxlsx'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.0/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.0\library" "C:/Users/rgowriga/Downloads/openxlsx_4.0.17.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/rgowriga/Downloads/openxlsx_4.0.17.tar.gz’ had non-zero exit status

digest package not installing in R - lgfortran not found

I am trying to install the digest package in R. However the installation is failing, apparently because the compiler does not recognize the -lgfortran flag. I have been unable to find any information on this. Any help is appreciated.
> install.packages('digest', repos='http://cran.us.r-project.org')
trying URL 'http://cran.us.r-project.org/src/contrib/digest_0.6.12.tar.gz'
Content type 'application/x-gzip' length 120337 bytes (117 KB)
==================================================
downloaded 117 KB
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c aes.c -o aes.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c crc32.c -o crc32.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c digest.c -o digest.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c init.c -o init.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c md5.c -o md5.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c pmurhash.c -o pmurhash.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c raes.c -o raes.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c sha1.c -o sha1.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c sha2.c -o sha2.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c sha256.c -o sha256.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -L/home/alexander/anaconda3/lib/R/lib -L/home/alexander/anaconda3/lib -lgfortran -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/home/alexander/anaconda3/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
/home/alexander/anaconda3/lib/R/share/make/shlib.mk:6: recipe for target 'digest.so' failed
make: *** [digest.so] Error 1
ERROR: compilation failed for package ‘digest’
* removing ‘/home/alexander/anaconda3/lib/R/library/digest’
* restoring previous ‘/home/alexander/anaconda3/lib/R/library/digest’
use homebrew to install gcc, gfortrain
Create folder /Users/YOURNAME/.R
Create text file /Users/YOURNAME/.R/Makevars
Put this into that file:
FC = usr/local/opt/gcc/bin/gfortran
F77 = /usr/local/opt/gcc/bin/gfortran
FLIBS = -L/usr/local/opt/gcc/lib

R install package Rcplex

I already follow INSTALL STEP at INSTALL
but something wrong happen when I install the package
c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-33~1.1/include" -DNDEBUG -I"C:/Program Files/IBM/ILOG/CPLEX_Studio_Community1263/cplex/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rcplex.c -o Rcplex.o
c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-33~1.1/include" -DNDEBUG -I"C:/Program Files/IBM/ILOG/CPLEX_Studio_Community1263/cplex/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rcplex_QCP.c -o Rcplex_QCP.o
Rcplex_QCP.c: In function 'Rcplex_QCP':
Rcplex_QCP.c:37:7: warning: unused variable 'trace' [-Wunused-variable]
int trace = INTEGER(getListElement(control,"trace"))[0];
^
c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-33~1.1/include" -DNDEBUG -I"C:/Program Files/IBM/ILOG/CPLEX_Studio_Community1263/cplex/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rcplex_params.c -o Rcplex_params.o
c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-33~1.1/include" -DNDEBUG -I"C:/Program Files/IBM/ILOG/CPLEX_Studio_Community1263/cplex/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rcplex_utils.c -o Rcplex_utils.o
C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lcplex1263
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'Rcplex'
When you go to the package documentation at: https://cran.r-project.org/web/packages/Rcplex/index.html ... You make no mention of satisfying the system requirements:
SystemRequirements: IBM ILOG CPLEX libraries and headers
The linker that gcc uses, ld, cannot find the shared library for CPLEX. According to the INSTALL document, you need to verify that CPLEX_LIB_PATH is defined to point to the path where the CPLEX dll's are located. From your output, I'd venture
set CPLEX_LIB_PATH="C:/Program Files/IBM/ILOG/CPLEX_Studio_Community1263/cplex/lib"
is what you need.

Error installing Kernlab from Source on MacOS X (lazy loading failed)

I have been trying to install the R package, Kernlab from source, but I have been running into problems. At first, I had some error related to gfortran, so I downloaded the GNU fortran compiler from http://r.research.att.com/tools/
Then when I type the following command: R CMD INSTALL kernlab_0.9-12.tar.gz
I get the following error:
installing to /Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) :
the "superClass" list for class "list", includes an undefined class "input"
Error in .walkClassGraph(ClassDef, "contains", where, attr(ext, "conflicts")) :
the "superClass" list for class "numeric", includes an undefined class "output"
Error : evaluation nested too deeply: infinite recursion / options(expressions=)?
Error in setClassUnion("listI", c("list", "numeric", "vector", "integer", :
unable to create union class: could not set members "list", "numeric"
Error : unable to load R code in package 'kernlab'
ERROR: lazy loading failed for package ‘kernlab’
* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/kernlab’
Does anyone know how to solve this error? PS. For the GNU fortran compiler I downloaded, it says that is for Xcode version up to 3.2.5; and I have Xcode version 3.2.6. Is this the source of my error, or am I looking in the wrong direction?
It must be something with your system. On my Linux box, kernlab_0.9-12 installs fine:
edd#max:/tmp$ R CMD INSTALL kernlab_0.9-12.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘kernlab’ ...
** libs
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c brweight.cpp -o brweight.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c ctable.cpp -o ctable.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c cweight.cpp -o cweight.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dbreakpt.c -o dbreakpt.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dcauchy.c -o dcauchy.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpnrm.c -o dgpnrm.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dgpstep.c -o dgpstep.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprecond.c -o dprecond.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dprsrch.c -o dprsrch.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dspcg.c -o dspcg.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtron.c -o dtron.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrpcg.c -o dtrpcg.o
dtrpcg.c: In function ‘dtrpcg’:
dtrpcg.c:157: warning: value computed is not used
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c dtrqsol.c -o dtrqsol.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c esa.cpp -o esa.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c expdecayweight.cpp -o expdecayweight.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c inductionsort.cpp -o inductionsort.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c kspectrumweight.cpp -o kspectrumweight.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c lcp.cpp -o lcp.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c misc.c -o misc.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c msufsort.cpp -o msufsort.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c solvebqp.c -o solvebqp.o
gcc-4.4 -I/usr/share/R/include -fpic -O3 -g0 -Wall -pipe -pedantic -std=gnu99 -c stringk.c -o stringk.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c stringkernel.cpp -o stringkernel.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c svm.cpp -o svm.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c wkasailcp.cpp -o wkasailcp.o
g++-4.4 -I/usr/share/R/include -fpic -O3 -pipe -c wmsufsort.cpp -o wmsufsort.o
g++ -shared -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR
installing to /usr/local/lib/R/site-library/kernlab/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "terms" in "kernlab"
Creating a new generic function for "fitted" in "kernlab"
Creating a new generic function for "coef" in "kernlab"
Creating a new generic function for "predict" in "kernlab"
Creating a new generic function for "plot" in "kernlab"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (kernlab)
edd#max:/tmp$
Moreover, it has nothing to do with gfortran as the package seems to contain only C and C++ files.
I doubt that a minor version shift in Xcode is the source of your problem (with the unstated version of fortran ... and the unstated version of R), but why not just install the Mac binary?
http://cran.r-project.org/bin/macosx/leopard/contrib/r-release/kernlab_0.9-12.tgz

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