• using R Under development (unstable) (2026-05-03 r89994)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 22.1.4 (https://github.com/llvm/llvm-project 35990504507d79e0b9deb809c8ee5e1b34ceef20)     flang version 22.1.4 (https://github.com/llvm/llvm-project 35990504507d79e0b9deb809c8ee5e1b34ceef20)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-05-04 07:55:08 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘clustTMB/DESCRIPTION’ ... OK
• this is package ‘clustTMB’ version ‘0.1.0’
• 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 ‘clustTMB’ can be installed ... [4m/10m] OK See the install log for details.
• used C++ compiler: ‘clang version 22.1.4 (https://github.com/llvm/llvm-project 35990504507d79e0b9deb809c8ee5e1b34ceef20)’
• checking installed package size ... INFO   installed size is 6.0Mb   sub-directories of 1Mb or more:     libs 5.5Mb
• 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 ... [6s/12s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/16s] OK
• checking whether the package can be unloaded cleanly ... [5s/17s] OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... [6s/18s] OK
• checking loading without being on the library search path ... [6s/23s] 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 ... [34s/141s] OK
• checking Rd files ... 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 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 ... [9s/37s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [0m/90m] ERROR   Running ‘testthat.R’ [0m/90m] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(clustTMB)   >   > test_check("clustTMB")   Loading required package: mclust   Package 'mclust' version 6.1.2   Type 'citation("mclust")' for citing this R package in publications.   Loading required package: MoEClust      Package 'MoEClust' version 1.6.0.      Type '?MoEClust' to see a brief guide to how to use this R package.   Type 'citation("MoEClust")' for citing the package in publications.   Type 'MoE_news()' to see new features recent changes and bug fixes.      Loading required package: mvnfast   Loading required package: FMsmsnReg   Loading required package: TMB   using C++ compiler: 'clang version 22.1.4 (https://github.com/llvm/llvm-project 35990504507d79e0b9deb809c8ee5e1b34ceef20)'   make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/clustTMB.Rcheck/tests/testthat'   clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"/data/gannet/ripley/R/test-clang/TMB/include" -I"/tmp/Rtmpjy28ot/RLIBS_c47256707438c/RcppEigen/include" -DTMB_SAFEBOUNDS -DTMB_EIGEN_DISABLE_WARNINGS -DLIB_UNLOAD=R_unload_simple -DTMB_LIB_INIT=R_init_simple -DCPPAD_FRAMEWORK -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ref/simple.cpp -o ref/simple.o   In file included from ref/simple.cpp:2:   In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:   In file included from /tmp/Rtmpjy28ot/RLIBS_c47256707438c/RcppEigen/include/Eigen/Sparse:26:   In file included from /tmp/Rtmpjy28ot/RLIBS_c47256707438c/RcppEigen/include/Eigen/SparseCore:61:   /tmp/Rtmpjy28ot/RLIBS_c47256707438c/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 ref/simple.cpp:2:   In file included from /data/gannet/ripley/R/test-clang/TMB/include/TMB.hpp:96:   In file included from /tmp/Rtmpjy28ot/RLIBS_c47256707438c/RcppEigen/include/Eigen/Sparse:29:   In file included from /tmp/Rtmpjy28ot/RLIBS_c47256707438c/RcppEigen/include/Eigen/SparseLU:35:   /tmp/Rtmpjy28ot/RLIBS_c47256707438c/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/Rtmpjy28ot/RLIBS_c47256707438c/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++-22 -stdlib=libc++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o ref/simple.so ref/simple.o   make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/clustTMB.Rcheck/tests/testthat'   make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/clustTMB.Rcheck/tests/testthat'   make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/clustTMB.Rcheck/tests/testthat'
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [1m/62m] ERROR Error(s) in re-building vignettes: --- re-building ‘CovarianceStructure.Rmd’ using rmarkdown --- finished re-building ‘CovarianceStructure.Rmd’ Warning: elapsed-time limit of 1 hours reached for sub-process --- re-building ‘SpatialExMeuseData.Rmd’ using rmarkdown OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead. OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set). SUMMARY: processing the following file failed:   ‘SpatialExMeuseData.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [7s/19s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs