- using R Under development (unstable) (2024-06-26 r86840)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 18.1.8 (1)
Debian flang-new version 18.1.8 (1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘epigrowthfit/DESCRIPTION’ ... OK
- this is package ‘epigrowthfit’ version ‘0.15.3’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘epigrowthfit’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘Debian clang version 18.1.8 (1)’
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
- checking loading without being on the library search path ... [2s/3s] OK
- checking whether startup messages can be suppressed ... [2s/3s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [35s/41s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking examples ... [21s/24s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [320s/397s] ERROR
Running ‘coef.R’ [4s/5s]
Running ‘confint.R’ [25s/40s]
Running ‘datetime.R’ [2s/2s]
Running ‘egf.R’ [5s/5s]
Running ‘egf_enum.R’ [3s/3s]
Running ‘egf_eval.R’ [2s/3s]
Running ‘egf_examples_day_of_week.R’ [3s/3s]
Running ‘egf_examples_excess.R’ [3s/3s]
Running ‘egf_examples_fixed.R’ [3s/3s]
Running ‘egf_examples_random.R’ [42s/48s]
Running ‘egf_link.R’ [2s/3s]
Running ‘egf_misc.R’ [5s/6s]
Running ‘egf_options.R’ [2s/3s]
Running ‘egf_utils.R’ [5s/6s]
Running ‘epidemic.R’ [2s/3s]
Running ‘extract.R’ [5s/5s]
Running ‘fitted.R’ [5s/6s]
Running ‘gi.R’ [3s/3s]
Running ‘include.R’ [167s/197s]
Running ‘language.R’ [2s/3s]
Running ‘prior.R’ [2s/3s]
Running ‘profile.R’ [16s/29s]
Running ‘summary.R’ [5s/5s]
Running ‘utils.R’ [2s/3s]
Running ‘validity.R’ [2s/3s]
Running ‘zzz.R’ [2s/3s]
Running the tests in ‘tests/include.R’ failed.
Complete output:
> library(epigrowthfit)
> options(warn = 2L, error = if (interactive()) recover)
>
> src <- "src"
> src. <- system.file("tests", src, package = "epigrowthfit", mustWork = TRUE)
> file.copy(c(src, src.), tempdir(), recursive = TRUE)
[1] TRUE TRUE
> setwd(file.path(tempdir(), src))
> Sys.setenv(R_TESTS = "") # startup.Rs does not exist here
>
> dll <- "test"
> cpp <- paste0(dll, ".cpp")
> TMB::compile(cpp)
Note: Using Makevars in /home/hornik/.R/Makevars-clang
using C++ compiler: 'Debian clang version 18.1.8 (1)'
make[1]: Entering directory '/tmp/RtmpiGpbyu/src'
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include" -I"/tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include" -DTMB_SAFEBOUNDS -DTMB_EIGEN_DISABLE_WARNINGS -DLIB_UNLOAD=R_unload_test -DTMB_LIB_INIT=R_init_test -DCPPAD_FRAMEWORK -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c test.cpp -o test.o
In file included from test.cpp:1:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:96:
In file included from /tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include/Eigen/Sparse:26:
In file included from /tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include/Eigen/SparseCore:61:
/tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from test.cpp:1:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TMB/include/TMB.hpp:96:
In file included from /tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include/Eigen/Sparse:29:
In file included from /tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include/Eigen/SparseLU:35:
/tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/tmp/RtmpskxQtq/RLIBS_328317900188f/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
3 warnings generated.
clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o test.so test.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpiGpbyu/src'
make[1]: Entering directory '/tmp/RtmpiGpbyu/src'
make[1]: Leaving directory '/tmp/RtmpiGpbyu/src'
[1] 0
> dyn.load(paste0(dll, .Platform[["dynlib.ext"]]))
>
> getReport <- local({
+ tt <- readLines(cpp)
+ tt <- paste(tt, collapse = "\n")
+ tt <- chartr("\t\r\n", " ", tt)
+ tt <- sub("^.*?enum +test *\\{(.*?)\\} *;.*$", "\\1", tt)
+ tt <- gsub(" ", "", tt)
+ enum. <- strsplit(tt, ",")[[1L]]
+
+ function(enum, ...)
+ TMB::MakeADFun(data = list(flag = match(enum, enum., 0L) - 1L, ...),
+ parameters = list(),
+ type = "Fun",
+ checkParameterOrder = FALSE,
+ DLL = dll)[["report"]]()[["ans"]]
+ })
>
> mvlgamma <- function(x, p)
+ 0.25 * p * (p - 1) * log(pi) + rowSums(lgamma(outer(x, seq.int(0, by = 0.5, length.out = p), `-`)))
>
> dlkj <- function(x, eta, log = FALSE) {
+ n <- 0.5 * (1 + sqrt(1 + 8 * length(x)))
+ R <- diag(n)
+ R[upper.tri(R)] <- x
+ log.ans <- (eta - 1) * (-sum(log(colSums(R * R))))
+ if (log) log.ans else exp(log.ans)
+ }
>
> dwishart <- function(x, df, scale, log = FALSE) {
+ n <- 0.5 * (-1 + sqrt(1 + 8 * length(x)))
+ X <- theta2cov(x)
+ S <- theta2cov(scale)
+ log.ans <- -0.5 * (df * log(det(S)) + (-df + n + 1) * log(det(X)) + n * df * log(2) + 2 * mvlgamma(0.5 * df, n) + sum(diag(solve(S, X))))
+ if (log) log.ans else exp(log.ans)
+ }
>
> dinvwishart <- function(x, df, scale, log = FALSE) {
+ n <- 0.5 * (-1 + sqrt(1 + 8 * length(x)))
+ X <- theta2cov(x)
+ S <- theta2cov(scale)
+ log.ans <- -0.5 * (-df * log(det(S)) + (df + n + 1) * log(det(X)) + n * df * log(2) + 2 * mvlgamma(0.5 * df, n) + sum(diag(solve(X, S))))
+ if (log) log.ans else exp(log.ans)
+ }
>
>
> ## list_of_vectors_t
> x <- list(rnorm(10L), seq_len(5L), TRUE, double(0L))
> ans <- getReport("list_of_vectors_t", x = x)
Error in isNullPointer(ADFun$ptr) :
R_ExternalPtrAddr: argument of type NILSXP is not an external pointer
Calls: getReport -> <Anonymous> -> f -> isNullPointer
Execution halted
- checking PDF version of manual ... [8s/10s] OK
- checking HTML version of manual ... [4s/6s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR