BMA

examples

Running examples in ‘BMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iBMA
> ### Title: Iterated Bayesian Model Averaging variable selection for
> ###   generalized linear models, linear models or survival models.
> ### Aliases: iBMA iBMA.glm iBMA.bicreg iBMA.surv iBMA.glm.data.frame
> ###   iBMA.glm.matrix iBMA.glm.iBMA.intermediate.glm iBMA.bicreg.data.frame
> ###   iBMA.bicreg.matrix iBMA.bicreg.iBMA.intermediate.bicreg
> ###   iBMA.surv.data.frame iBMA.surv.matrix
> ###   iBMA.surv.iBMA.intermediate.surv
> ### Keywords: regression survival
> 
> ### ** Examples
> 
> 
> ## Not run: 
> ##D ############ iBMA.glm
> ##D library("MASS")
> ##D data(birthwt)
> ##D  y<- birthwt$lo
> ##D  x<- data.frame(birthwt[,-1])
> ##D  x$race<- as.factor(x$race)
> ##D  x$ht<- (x$ht>=1)+0
> ##D  x<- x[,-9]
> ##D  x$smoke <- as.factor(x$smoke)
> ##D  x$ptl<- as.factor(x$ptl)
> ##D  x$ht <- as.factor(x$ht)
> ##D  x$ui <- as.factor(x$ui)
> ##D 
> ##D ### add 41 columns of noise
> ##D noise<- matrix(rnorm(41*nrow(x)), ncol=41)
> ##D colnames(noise)<- paste('noise', 1:41, sep='')
> ##D x<- cbind(x, noise)
> ##D 
> ##D iBMA.glm.out<- iBMA.glm( x, y, glm.family="binomial", 
> ##D                          factor.type=FALSE, verbose = TRUE, 
> ##D                          thresProbne0 = 5 )
> ##D summary(iBMA.glm.out)
> ## End(Not run)
> 
> ## Not run: 
> ##D ################## iBMA.surv
> ##D library(survival)
> ##D data(cancer)
> ##D 
> ##D surv.t<- veteran$time
> ##D cens<- veteran$status
> ##D veteran$time<- NULL
> ##D veteran$status<- NULL
> ##D lvet<- nrow(veteran)
> ##D invlogit<- function(x) exp(x)/(1+exp(x))
> ##D # generate random noise, 34 uniform variables 
> ##D # and 10 factors each with 4 levels
> ##D X <- data.frame(matrix(runif(lvet*34), ncol=34), 
> ##D                matrix(letters[1:6][(rbinom(10*lvet, 3, .5))+1], 
> ##D                ncol = 10))
> ##D colnames(X) <- c(paste("u",1:34, sep=""),paste("C",1:10, sep=""))
> ##D for(i in 35:44) X[,i] <- as.factor(X[,i])
> ##D veteran_plus_noise<- cbind(veteran, X)
> ##D 
> ##D 
> ##D test.iBMA.surv <- iBMA.surv(x = veteran_plus_noise, 
> ##D                             surv.t = surv.t, cens = cens, 
> ##D                             thresProbne0 = 5, maxNvar = 30, 
> ##D                             factor.type = TRUE, verbose = TRUE, 
> ##D                             nIter = 100)
> ##D 
> ##D test.iBMA.surv
> ##D summary(test.iBMA.surv)
> ## End(Not run)
> 
> ## Not run: 
> ##D ############ iBMA.bicreg ... degenerate example
> ##D library(MASS)
> ##D data(UScrime)
> ##D UScrime$M<- log(UScrime$M); UScrime$Ed<- log(UScrime$Ed); 
> ##D UScrime$Po1<- log(UScrime$Po1); UScrime$Po2<- log(UScrime$Po2); 
> ##D UScrime$LF<- log(UScrime$LF); UScrime$M.F<- log(UScrime$M.F)
> ##D UScrime$Pop<- log(UScrime$Pop); UScrime$NW<- log(UScrime$NW); 
> ##D UScrime$U1<- log(UScrime$U1); UScrime$U2<- log(UScrime$U2); 
> ##D UScrime$GDP<- log(UScrime$GDP); UScrime$Ineq<- log(UScrime$Ineq)
> ##D UScrime$Prob<- log(UScrime$Prob); UScrime$Time<- log(UScrime$Time) 
> ##D noise<- matrix(rnorm(35*nrow(UScrime)), ncol=35)
> ##D colnames(noise)<- paste('noise', 1:35, sep='')
> ##D UScrime_plus_noise<- cbind(UScrime, noise)
> ##D 
> ##D y<- UScrime_plus_noise$y
> ##D UScrime_plus_noise$y <- NULL
> ##D 
> ##D # run 2 iterations and examine results
> ##D iBMA.bicreg.crime <- iBMA.bicreg( x = UScrime_plus_noise, 
> ##D  Y = y, thresProbne0 = 5, verbose = TRUE, maxNvar = 30, nIter = 2)
> ##D summary(iBMA.bicreg.crime)
> ##D orderplot(iBMA.bicreg.crime)
> ## End(Not run)
> 
> ## Not run: 
> ##D # run from current state until completion
> ##D iBMA.bicreg.crime <- iBMA.bicreg( iBMA.bicreg.crime, nIter = 200)
> ##D summary(iBMA.bicreg.crime)
> ##D orderplot(iBMA.bicreg.crime)
> ## End(Not run)
> 
> set.seed(0)
> x <- matrix( rnorm(50*30), 50, 30)
> lp <- apply( x[,1:5], 1, sum)
> iBMA.bicreg.ex <- iBMA.bicreg( x = x,  Y = lp, thresProbne0 = 5, maxNvar = 20)
> 
> explp <- exp(lp)
> prob <- explp/(1+explp)
> y=rbinom(n=length(prob),prob=prob,size=1)
> iBMA.glm.ex <- iBMA.glm( x = x, Y = y, glm.family = "binomial",
+                          factor.type = FALSE, thresProbne0 = 5, maxNvar = 20)

ERROR(s) during compilation: source code errors or compiler configuration errors!
make cmd is
  make -f '/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf' -f '/home/hornik/tmp/R.check/r-devel-clang/Work/build/share/make/shlib.mk' -f '/home/hornik/.R/Makevars-clang' SHLIB='file319a5320b5ac6e.so' OBJECTS='file319a5320b5ac6e.o'

make would use
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpPmKxDh'
clang-21 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c file319a5320b5ac6e.c -o file319a5320b5ac6e.o
if test  "zfile319a5320b5ac6e.o" != "z"; then \
  echo clang-21 -std=gnu23 -shared -L"/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib" -Wl,-O1 -o file319a5320b5ac6e.so file319a5320b5ac6e.o    -L"/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib" -lR; \
  clang-21 -std=gnu23 -shared -L"/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib" -Wl,-O1 -o file319a5320b5ac6e.so file319a5320b5ac6e.o    -L"/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib" -lR; \
fi
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpPmKxDh'

Program source:
  1: #include <R.h>
  2: #include <Rdefines.h>
  3: #include <R_ext/Error.h>
  4: 
  5: 
  6: /* This is taken from envir.c in the R 2.15.1 source
  7: https://github.com/SurajGupta/r-source/blob/master/src/main/envir.c
  8: */
  9: #define FRAME_LOCK_MASK (1<<14)
 10: #define FRAME_IS_LOCKED(e) (ENVFLAGS(e) & FRAME_LOCK_MASK)
 11: #define UNLOCK_FRAME(e) SET_ENVFLAGS(e, ENVFLAGS(e) & (~ FRAME_LOCK_MASK))
 12: #define R_NO_REMAP
 13: 
 14: 
 15: SEXP file319a5320b5ac6e ( SEXP env ) {
 16: 
 17: if (TYPEOF(env) == NILSXP)
 18: Rf_error("use of NULL environment is defunct");
 19: if (TYPEOF(env) != ENVSXP)
 20: Rf_error("not an environment");
 21:  
 22: UNLOCK_FRAME(env);
 23:  
 24: // Return TRUE if unlocked; FALSE otherwise
 25: SEXP result = PROTECT( Rf_allocVector(LGLSXP, 1) );
 26: LOGICAL(result)[0] = FRAME_IS_LOCKED(env) == 0;
 27: UNPROTECT(1);
 28:  
 29: return result;
 30: 
 31:   Rf_warning("your C program does not return anything!");
 32:   return R_NilValue;
 33: }

Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language, verbose) : 
  from macro 'UNLOCK_FRAME'
   11 | #define UNLOCK_FRAME(e) SET_ENVFLAGS(e, ENVFLAGS(e) & (~ FRAME_LOCK_MASK))
      |                         ^~~~~~~~~~~~
file319a5320b5ac6e.c:22:1: error: use of undeclared identifier 'ENVFLAGS'
   22 | UNLOCK_FRAME(env);
      | ^~~~~~~~~~~~~~~~~
file319a5320b5ac6e.c:11:41: note: expanded from macro 'UNLOCK_FRAME'
   11 | #define UNLOCK_FRAME(e) SET_ENVFLAGS(e, ENVFLAGS(e) & (~ FRAME_LOCK_MASK))
      |                                         ^~~~~~~~
file319a5320b5ac6e.c:26:22: error: use of undeclared identifier 'ENVFLAGS'
   26 | LOGICAL(result)[0] = FRAME_IS_LOCKED(env) == 0;
      |                      ^~~~~~~~~~~~~~~~~~~~
file319a5320b5ac6e.c:10:29: note: expanded from macro 'FRAME_IS_LOCKED'
   10 | #define FRAME_IS_LOCKED(e) (ENVFLAGS(e) & FRAME_LOCK_MASK)
      |                             ^~~~~~~~
1 warning and 3 errors generated.
make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: file319a5320b5ac6e.o
Calls: iBMA.glm -> iBMA.glm.matrix -> cfunction -> compileCode
Execution halted

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