Last updated on 2025-01-15 05:50:16 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.18.20 | 16.01 | 109.21 | 125.22 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.18.20 | 11.82 | 72.35 | 84.17 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.18.20 | 204.92 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.18.20 | 202.94 | OK | |||
| r-devel-windows-x86_64 | 3.18.20 | 20.00 | 112.00 | 132.00 | OK | |
| r-patched-linux-x86_64 | 3.18.19 | 16.29 | 99.85 | 116.14 | OK | |
| r-release-linux-x86_64 | 3.18.19 | 14.21 | 99.34 | 113.55 | OK | |
| r-release-macos-arm64 | 3.18.20 | 52.00 | OK | |||
| r-release-macos-x86_64 | 3.18.20 | 148.00 | OK | |||
| r-release-windows-x86_64 | 3.18.19 | 20.00 | 105.00 | 125.00 | ERROR | |
| r-oldrel-macos-arm64 | 3.18.20 | 54.00 | OK | |||
| r-oldrel-macos-x86_64 | 3.18.20 | 148.00 | OK | |||
| r-oldrel-windows-x86_64 | 3.18.20 | 23.00 | 142.00 | 165.00 | OK |
Version: 3.18.19
Check: examples
Result: ERROR
Running examples in 'BMA-Ex.R' failed
The error most likely occurred in:
> ### 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 "D:/RCompile/recent/R-4.4.2/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.4.2/share/make/winshlib.mk" SHLIB="file2879c12ec536d.dll" WIN=64 TCLBIN= OBJECTS="file2879c12ec536d.o"
make would use
make[1]: Entering directory '/d/temp/2025_01_11_01_50_00_344/RtmpATXTaU'
if test "zfile2879c12ec536d.o" != "z"; then \
if test -e "file2879c12ec536d-win.def"; then \
echo gcc -shared -s -static-libgcc -o file2879c12ec536d.dll file2879c12ec536d-win.def file2879c12ec536d.o -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R-4.4.2/bin/x64" -lR ; \
gcc -shared -s -static-libgcc -o file2879c12ec536d.dll file2879c12ec536d-win.def file2879c12ec536d.o -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R-4.4.2/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm file2879c12ec536d.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \
echo gcc -shared -s -static-libgcc -o file2879c12ec536d.dll tmp.def file2879c12ec536d.o -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R-4.4.2/bin/x64" -lR ; \
gcc -shared -s -static-libgcc -o file2879c12ec536d.dll tmp.def file2879c12ec536d.o -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools44/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R-4.4.2/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2025_01_11_01_50_00_344/RtmpATXTaU'
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 file2879c12ec536d ( 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.exe (GCC) 13.3.0'
file2879c12ec536d.c: In function 'file2879c12ec536d':
file2879c12ec536d.c:17:1: warning: implicit declaration of function 'error'; did you mean 'ferror'? [-Wimplicit-function-declaration]
17 | error("use of NULL environment is defunct");
| ^~~~~
| ferror
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: file2879c12ec536d.o:file2879c12ec536d.c:(.text+0x27): undefined reference to `error'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: file2879c12ec536d.o:file2879c12ec536d.c:(.text+0x98): undefined reference to `error'
collect2.exe: error: ld returned 1 exit status
Calls: iBMA.glm -> iBMA.glm.matrix -> cfunction -> compileCode
Execution halted
Flavor: r-release-windows-x86_64