* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/BOSO.Rcheck’ * using R Under development (unstable) (2024-03-16 r86144) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘BOSO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BOSO’ version ‘1.0.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Packages suggested but not available for checking: 'cplexAPI', 'bestsubset' * 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 ‘BOSO’ can be installed ... OK * 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 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 ... [15s/20s] 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 ... NOTE Documented arguments not in \usage in Rd file 'InternalFunctions.Rd': ‘metric’ ‘matrix’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘BOSO-Ex.R’ failed The error most likely occurred in: > ### Name: BOSO > ### Title: BOSO and associates functions > ### Aliases: BOSO > > ### ** Examples > > > #This first example is a basic > #example of how to execute BOSO > > ## No test: > data("sim.xy", package = "BOSO") > obj <- BOSO(x = sim.xy[['low']]$x, + y = sim.xy[['low']]$y, + xval = sim.xy[['low']]$xval, + yval = sim.xy[['low']]$yval, + IC = 'eBIC', + nlambda=50, + intercept= 0, standardize = 0, + Threads=1, verbose = 3, seed = 2021) Error: Package cplexAPI not installed (required here)! Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [27s/35s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘BOSO.Rmd’ using rmarkdown Quitting from lines 475-492 [plot_comparison_BOSOvsREST] (BOSO.Rmd) Error: processing vignette 'BOSO.Rmd' failed with diagnostics: The `legend.pos` theme element is not defined in the element hierarchy. --- failed re-building ‘BOSO.Rmd’ SUMMARY: processing the following file failed: ‘BOSO.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [6s/10s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/data/blackswan/ripley/R/packages/tests-devel/BOSO.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:40.60, 101.94 + 13.77