- using R Under development (unstable) (2026-05-19 r90065)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
* current time: 2026-05-21 08:49:21 UTC
- using option ‘--no-stop-on-test-error’
- checking for file ‘gkwreg/DESCRIPTION’ ... OK
- this is package ‘gkwreg’ version ‘2.1.14’
- 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 ‘gkwreg’ can be installed ... [64s/196s] OK
See the install log for details.
- used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
- checking C++ specification ... INFO
specified C++17
- checking package directory ... OK
- checking ‘build’ directory ... 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/12s] OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... [3s/16s] 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 ... [37s/162s] OK
- checking Rd files ... [2s/14s] 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 ... 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [4s/13s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [5s/18s] OK
Running ‘testthat.R’ [5s/15s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [8m/91m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘gkwreg-vs-betareg.Rmd’ using rmarkdown
make[1]: Entering directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/gkwbetareg_compile_20260521_100344'
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"/data/gannet/ripley/R/test-dev/TMB/include" -I"/data/gannet/ripley/R/test-dev/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_gkwbetareg -DCPPAD_FRAMEWORK -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c gkwbetareg.cpp -o gkwbetareg.o
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o gkwbetareg.so gkwbetareg.o
make[1]: Leaving directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/gkwbetareg_compile_20260521_100344'
make[1]: Entering directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/gkwbetareg_compile_20260521_100344'
make[1]: Leaving directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/gkwbetareg_compile_20260521_100344'
make[1]: Entering directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/kwreg_compile_20260521_101624'
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"/data/gannet/ripley/R/test-dev/TMB/include" -I"/data/gannet/ripley/R/test-dev/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_kwreg -DCPPAD_FRAMEWORK -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kwreg.cpp -o kwreg.o
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o kwreg.so kwreg.o
make[1]: Leaving directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/kwreg_compile_20260521_101624'
make[1]: Entering directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/kwreg_compile_20260521_101624'
make[1]: Leaving directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/kwreg_compile_20260521_101624'
make[1]: Entering directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/ekwreg_compile_20260521_104835'
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"/data/gannet/ripley/R/test-dev/TMB/include" -I"/data/gannet/ripley/R/test-dev/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_ekwreg -DCPPAD_FRAMEWORK -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ekwreg.cpp -o ekwreg.o
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o ekwreg.so ekwreg.o
make[1]: Leaving directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/ekwreg_compile_20260521_104835'
make[1]: Entering directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/ekwreg_compile_20260521_104835'
make[1]: Leaving directory '/tmp/Rtmpo51QWr/working_dir/RtmpnFaAFR/ekwreg_compile_20260521_104835'
Quitting from gkwreg-vs-betareg.Rmd:586-599 [scenario1_sim]
Execution halted
- checking PDF version of manual ... [13s/34s] OK
- checking HTML version of manual ... [14s/50s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR