Last updated on 2024-08-16 20:48:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.18.17 | 16.03 | 101.23 | 117.26 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.18.17 | 11.30 | 64.83 | 76.13 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.18.17 | 191.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.18.17 | 182.14 | OK | |||
| r-devel-windows-x86_64 | 3.18.17 | 19.00 | 109.00 | 128.00 | OK | |
| r-patched-linux-x86_64 | 3.18.17 | 15.89 | 95.15 | 111.04 | OK | |
| r-release-linux-x86_64 | 3.18.17 | 14.78 | 96.54 | 111.32 | OK | |
| r-release-macos-arm64 | 3.18.17 | 51.00 | OK | |||
| r-release-macos-x86_64 | 3.18.17 | 83.00 | OK | |||
| r-release-windows-x86_64 | 3.18.17 | 19.00 | 110.00 | 129.00 | OK | |
| r-oldrel-macos-arm64 | 3.18.17 | 57.00 | OK | |||
| r-oldrel-macos-x86_64 | 3.18.17 | 93.00 | OK | |||
| r-oldrel-windows-x86_64 | 3.18.17 | 24.00 | 138.00 | 162.00 | OK |
Version: 3.18.17
Check: examples
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$ui)
> ##D
> ##D ### add 41 columns of noise
> ##D noise<- matrix(rnorm(41*nrow(x)), ncol=41)
> ##D colnames(noise)<- paste('noise', 1:41, sep='')
> ##D x<- cbind(x, noise)
> ##D
> ##D iBMA.glm.out<- iBMA.glm( x, y, glm.family="binomial",
> ##D factor.type=FALSE, verbose = TRUE,
> ##D thresProbne0 = 5 )
> ##D summary(iBMA.glm.out)
> ## End(Not run)
>
> ## Not run:
> ##D ################## iBMA.surv
> ##D library(survival)
> ##D data(veteran)
> ##D
> ##D surv.t<- veteran$time
> ##D cens<- veteran$status
> ##D veteran$time<- NULL
> ##D veteran$status<- NULL
> ##D lvet<- nrow(veteran)
> ##D invlogit<- function(x) exp(x)/(1+exp(x))
> ##D # generate random noise, 34 uniform variables
> ##D # and 10 factors each with 4 levels
> ##D X <- data.frame(matrix(runif(lvet*34), ncol=34),
> ##D matrix(letters[1:6][(rbinom(10*lvet, 3, .5))+1],
> ##D ncol = 10))
> ##D colnames(X) <- c(paste("u",1:34, sep=""),paste("C",1:10, sep=""))
> ##D veteran_plus_noise<- cbind(veteran, X)
> ##D
> ##D
> ##D test.iBMA.surv <- iBMA.surv(x = veteran_plus_noise,
> ##D surv.t = surv.t, cens = cens,
> ##D thresProbne0 = 5, maxNvar = 30,
> ##D factor.type = TRUE, verbose = TRUE,
> ##D nIter = 100)
> ##D
> ##D test.iBMA.surv
> ##D summary(test.iBMA.surv)
> ## End(Not run)
>
> ## Not run:
> ##D ############ iBMA.bicreg ... degenerate example
> ##D library(MASS)
> ##D data(UScrime)
> ##D UScrime$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$y <- NULL
> ##D
> ##D # run 2 iterations and examine results
> ##D iBMA.bicreg.crime <- iBMA.bicreg( x = UScrime_plus_noise,
> ##D Y = y, thresProbne0 = 5, verbose = TRUE, maxNvar = 30, nIter = 2)
> ##D summary(iBMA.bicreg.crime)
> ##D orderplot(iBMA.bicreg.crime)
> ## End(Not run)
>
> ## Not run:
> ##D # run from current state until completion
> ##D iBMA.bicreg.crime <- iBMA.bicreg( iBMA.bicreg.crime, nIter = 200)
> ##D summary(iBMA.bicreg.crime)
> ##D orderplot(iBMA.bicreg.crime)
> ## End(Not run)
>
> set.seed(0)
> x <- matrix( rnorm(50*30), 50, 30)
> lp <- apply( x[,1:5], 1, sum)
> iBMA.bicreg.ex <- iBMA.bicreg( x = x, Y = lp, thresProbne0 = 5, maxNvar = 20)
>
> explp <- exp(lp)
> prob <- explp/(1+explp)
> y=rbinom(n=length(prob),prob=prob,size=1)
> iBMA.glm.ex <- iBMA.glm( x = x, Y = y, glm.family = "binomial",
+ factor.type = FALSE, thresProbne0 = 5, maxNvar = 20)
ERROR(s) during compilation: source code errors or compiler configuration errors!
make cmd is
make -f '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/etc/Makeconf' -f '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/share/make/shlib.mk' -f '/home/hornik/.R/Makevars-gcc' SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB='file1473886acb03d8.so' CXX_DEFS=-DR_NO_REMAP XDEFS=-DSTRICT_R_HEADERS=1 OBJECTS='file1473886acb03d8.o'
make would use
make[1]: Entering directory '/tmp/RtmpH7fzJt'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c file1473886acb03d8.cpp -o file1473886acb03d8.o
if test "zfile1473886acb03d8.o" != "z"; then \
echo g++-14 -std=gnu++17 -shared -L"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib" -Wl,-O1 -o file1473886acb03d8.so file1473886acb03d8.o -L"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib" -lR; \
g++-14 -std=gnu++17 -shared -L"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib" -Wl,-O1 -o file1473886acb03d8.so file1473886acb03d8.o -L"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib" -lR; \
fi
make[1]: Leaving directory '/tmp/RtmpH7fzJt'
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: extern "C" {
15: SEXP file1473886acb03d8 ( SEXP env );
16: }
17:
18: SEXP file1473886acb03d8 ( SEXP env ) {
19:
20: if (TYPEOF(env) == NILSXP)
21: error("use of NULL environment is defunct");
22: if (TYPEOF(env) != ENVSXP)
23: error("not an environment");
24:
25: UNLOCK_FRAME(env);
26:
27: // Return TRUE if unlocked; FALSE otherwise
28: SEXP result = PROTECT( Rf_allocVector(LGLSXP, 1) );
29: LOGICAL(result)[0] = FRAME_IS_LOCKED(env) == 0;
30: UNPROTECT(1);
31:
32: return result;
33:
34: warning("your C program does not return anything!");
35: return R_NilValue;
36: }
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language, verbose) :
using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’file1473886acb03d8.cpp: In function ‘SEXPREC* file1473886acb03d8(SEXP)’:file1473886acb03d8.cpp:21:1: error: ‘error’ was not declared in this scope; did you mean ‘perror’? 21 | error("use of NULL environment is defunct"); | ^~~~~ | perrorfile1473886acb03d8.cpp:23:1: error: ‘error’ was not declared in this scope; did you mean ‘perror’? 23 | error("not an environment"); | ^~~~~ | perrorfile1473886acb03d8.cpp:34:3: error: ‘warning’ was not declared in this scope; did you mean ‘Rf_warning’? 34 | warning("your C program does not return anything!"); | ^~~~~~~ | Rf_warningmake[1]: *** [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/etc/Makeconf:204: file1473886acb03d8.o] Error 1
Calls: iBMA.glm -> iBMA.glm.matrix -> cfunction -> compileCode
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc