Package: BMA
Check: examples
New result: ERROR
  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/etc/Makeconf' -f '/home/hornik/tmp/R/share/make/shlib.mk' -f '/home/hornik/.R/Makevars-gcc' SHLIB='file2b118a307991ad.so' CXX_DEFS=-DR_NO_REMAP OBJECTS='file2b118a307991ad.o'
  
  make would use
  gcc-14  -I"/home/hornik/tmp/R/include" -DNDEBUG -DR_NO_REMAP  -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c file2b118a307991ad.c -o file2b118a307991ad.o
  if test  "zfile2b118a307991ad.o" != "z"; then \
    echo gcc-14  -shared -L"/home/hornik/tmp/R/lib" -Wl,-O1 -o file2b118a307991ad.so file2b118a307991ad.o    -L"/home/hornik/tmp/R/lib" -lR; \
    gcc-14  -shared -L"/home/hornik/tmp/R/lib" -Wl,-O1 -o file2b118a307991ad.so file2b118a307991ad.o    -L"/home/hornik/tmp/R/lib" -lR; \
  fi
  
  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: 
   13: 
   14: SEXP file2b118a307991ad ( SEXP env ) {
   15: 
   16: if (TYPEOF(env) == NILSXP)
   17: error("use of NULL environment is defunct");
   18: if (TYPEOF(env) != ENVSXP)
   19: error("not an environment");
   20:  
   21: UNLOCK_FRAME(env);
   22:  
   23: // Return TRUE if unlocked; FALSE otherwise
   24: SEXP result = PROTECT( Rf_allocVector(LGLSXP, 1) );
   25: LOGICAL(result)[0] = FRAME_IS_LOCKED(env) == 0;
   26: UNPROTECT(1);
   27:  
   28: return result;
   29: 
   30:   Rf_warning("your C program does not return anything!");
   31:   return R_NilValue;
   32: }
  
  Compilation ERROR, function(s)/method(s) not created!
  Error in compileCode(f, code, language, verbose) : 
    using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
  file2b118a307991ad.c: In function ‘file2b118a307991ad’:
  file2b118a307991ad.c:17:1: error: implicit declaration of function ‘error’; did you mean ‘perror’? [-Wimplicit-function-declaration]
     17 | error("use of NULL environment is defunct");
        | ^~~~~
        | perror
  make: *** [/home/hornik/tmp/R/etc/Makeconf:195: file2b118a307991ad.o] Error 1
  Calls: iBMA.glm -> iBMA.glm.matrix -> cfunction -> compileCode
  Execution halted