search for: rsvm

...of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether icpc accepts -g... yes ** libs icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -c Rsvm.c -o Rsvm.o icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -c cmeans.c -o cmeans.o icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -...

...compiler, and some diagnostic output showing the errors. >> >> Advice appreciated! >> >> Thanks, >> >> Andy > > There are two things missing when R tries to create the shared object > file on this line: > > icpc -L/usr/local/lib64 -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o > svm.o > > Firstly, the compiler flag "-shared" is missing. It tells the compiler > to build a shared object instead of an executable. Secondly the linker > flag "-lR" is missing, along with the "-L" flag that tells the link...

...low, there's information on my > platform, compiler, and some diagnostic output showing the errors. > > Advice appreciated! > > Thanks, > > Andy There are two things missing when R tries to create the shared object file on this line: icpc -L/usr/local/lib64 -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o svm.o Firstly, the compiler flag "-shared" is missing. It tells the compiler to build a shared object instead of an executable. Secondly the linker flag "-lR" is missing, along with the "-L" flag that tells the linker where to find the shar...

I observed the same behavior as Edward this morning with R-1.2.2 on Red Hat Linux 7.0. There appears to be a problem with the library in netpbm-9.5-5, even after hunting down the missing shhopt.h that pbmplus.h is looking for. I worked around the problem by compiling e1071 without pbm support (moved pbm.c to pbm.c.bak). Matt Matthew R. Nelson, Ph.D. Director, Information Systems Esperion

I observed the same behavior as Edward this morning with R-1.2.2 on Red Hat Linux 7.0. There appears to be a problem with the library in netpbm-9.5-5, even after hunting down the missing shhopt.h that pbmplus.h is looking for. I worked around the problem by compiling e1071 without pbm support (moved pbm.c to pbm.c.bak). Matt Matthew R. Nelson, Ph.D. Director, Information Systems Esperion

Hello, I'm using recursive SVM script (rSVM - http://www.stanford.edu/group/wonglab/RSVMpage/R-SVM.html ) on some microarray data. The data to be input are log2, as numeric matrix w/ attributes -- str(svm_num_mat) num [1:10, 1:12340] 13.1 13.1 13.1 13.1 13.0 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:10] "rma_log2...

...ing... 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++ accepts -g... yes ** libs gcc -I/app/R-1.9.0-p/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c Rsvm.c -o Rsvm.o gcc -I/app/R-1.9.0-p/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c cmeans.c -o cmeans.o gcc -I/app/R-1.9.0-p/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c cshell.c -o cshell.o gcc -I/app/R-1.9.0-p/lib/R/includ...

Dear All: I found a problem with the SVM internal cross-validation (CV) accuracy estimation in the e1071 package. File: Rsvm.c Line: 120 Today, it is: int j = rand()%(prob->l-i); Should be: int j = i + rand()%(prob->l-i); The erroneous code doesn't shuffle objects. Instead, it "randomly" moves objects from beginning to the end. In hope for a prompt response from the e1071 developer team, Thank...

...ut: a named list ## Error: a vector of CV error on each level ## SelFreq: a matrix for the frequency of each gene being selected in each level ## with each column corresponds to a level of selection ## and each row for a gene ## The top important gene in each level are those high-freqent ones RSVM <- function(x, y, ladder, CVtype, CVnum=0 ) { ## check if y is binary response Ytype <- names(table(y)) if( length(Ytype) != 2) { print("ERROR!! RSVM can only deal with 2-class problem") return(0) } ## class mean m1 <- apply(x[ which(y==Ytype[1]), ], 2, mean) m2 <-...

...t;predict.loess" [9] "predict.mlm" "predict.nls" [11] "predict.poly" "predict.ppr" [13] "predict.princomp" "predict.smooth.spline" [15] "predict.smooth.spline.fit" > setClass("RSVMState", + representation ( + kernel = "character", + rho = "numeric", + supportVector = "matrix", + alpha = "numeric...

.../users/local/lib/R/include -I/usr/local/include -KPIC -xlibmil \ -dalign -xO4 -c cshell.c -o cshell.o cc -I/users/local/lib/R/include -I/usr/local/include -KPIC -xlibmil \ -dalign -xO4 -c floyd.c -o floyd.o cc -I/users/local/lib/R/include -I/usr/local/include -KPIC -xlibmil \ -dalign -xO4 -c Rsvm.c -o Rsvm.o CC -I/users/local/lib/R/include -I/usr/local/include -KPIC -xlibmil \ -dalign -xO4 -c svm.cpp -o svm.o "svm.cpp", line 444: Warning: l hides Solver::l. "svm.cpp", line 444: Warning: Q hides Solver::Q. "svm.cpp", line 444: Warning: Cp hides Solver::Cp. &qu...

Hi list, Could someone help me to explain why the leave-one-out cross validation results I got from svm using the internal option "cross" are different from those I got manually? It seems using "cross" to do cross validation, the results are always better. Please see the code below. I also include lda as a comparison. I'm using WinXP, R-2.9.0, and e1071_1.5-19. Many

...I/usr/local/opt/x86_64-pc-solar is2.10/R-2.9.1/lib64/R/include -I/usr/local/include -fpic -g -O2 -c floyd.c -o floyd.o g++ -m64 -I/usr/local/opt/x86_64-pc-solaris2.10/R-2.9.1/lib64/R/include - I/usr/local/include -fpic -g -O2 -c svm.cpp -o svm.o g++ -m64 -G -L/usr/local/lib64 -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o svm. o ** R ** inst ** preparing package for lazy loading ** help *** installing help indices >>> Building/Updating help pages for package 'e1071' Formats: text html latex example Discrete text html latex example...

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