• using R Under development (unstable) (2026-09-25 r90590)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)     GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-09-27 23:02:44 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘ngme2/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ngme2’ version ‘1.0.0’
• 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 ‘ngme2’ can be installed ... [630s/164s] OK See the install log for details.
• used C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
• 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 ... 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 ... OK
• checking whether startup messages can be suppressed ... 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 ... [38s/40s] 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 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 ... INFO GNU make is a SystemRequirements.
• 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 include directives 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 ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [90m/48m] ERROR   Running ‘testthat.R’ [90m/48m] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   >   > library(testthat)   >   > test_check("ngme2")   Loading required package: ngme2   This is ngme2 of version 1.0.0   - See our homepage: https://davidbolin.github.io/ngme2 for more details.      Attaching package: 'ngme2'      The following object is masked from 'package:stats':          ar         stop 1:   ------------------------------------------------------------------------------------------------------------------------------------   Param: theta rho rho (1st) rho (2nd) mu_1 mu_2 sigma_1 sigma_2 nu_1 nu_2 meas_sigma_1   ------------------------------------------------------------------------------------------------------------------------------------   R_hat: 2.400 1.851 3.316 2.329 4.264 2.878 3.727 2.760 1.818 1.634 4.822   ------------------------------------------------------------------------------------------------------------------------------------      List of 6    $ mean : num [1:3] -1.123 0.367 -1.726    $ sd : num [1:3] 0.885 0.821 0.973    $ 0.05q : num [1:3] -2.8 -0.9 -3.28    $ 0.95q : num [1:3] 0.185 1.884 -0.146    $ median: num [1:3] -1.094 0.297 -1.73    $ mode : num [1:3] -1.3 0.3 -1.3    - attr(*, "samples")= num [1:10, 1:500] -2.508 -2.802 -3.934 0.585 0.665 ...   Starting estimation...   iteration = : 1   grad.norm() = 1.40988   ---------------------------   iteration = : 2   grad.norm() = 0.417141   ---------------------------   iteration = : 3   grad.norm() = 0.244426   ---------------------------   iteration = : 4   grad.norm() = 0.149198   ---------------------------   iteration = : 5   grad.norm() = 0.11251   ---------------------------   iteration = : 6   grad.norm() = 0.0915698   ---------------------------   iteration = : 7   grad.norm() = 0.0583889   ---------------------------   iteration = : 8   grad.norm() = 0.0856755   ---------------------------   iteration = : 9   grad.norm() = 0.0494385   ---------------------------   iteration = : 10   grad.norm() = 0.0554743   ---------------------------   [iter 10] 0/11 converged worst: R_hat 12.668 (mu_1), drift/100 0.00%              theta: theta=0.3880 rho=-0.0078 kappa (1st)=0.1928 kappa (2nd)=0.3614 mu_1=0.2692 mu_2=0.2073 sigma_1=-0.0700 sigma_2=-0.1551 nu_1=0.1640 nu_2=0.0670 meas_sigma_1=-0.6843   Starting posterior sampling...   Posterior sampling done.   Average standard deviation of the posterior W: 0.224301602161384   Use ngme_post_samples() to access posterior samples and ngme_result() to access latent model parameters.
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... OK
• checking PDF version of manual ... 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: 1 ERROR