* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/huge.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 18.1.4 flang-new version 18.1.4 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘huge/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘huge’ version ‘1.3.5’ * 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 ‘huge’ can be installed ... [133s/112s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/huge-00install.html' for details. * used C++ compiler: ‘clang version 18.1.4’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... 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 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 ... [24s/31s] OK * checking Rd files ... NOTE checkRd: (-1) huge.Rd:31: Lost braces; missing escapes or markup? 31 | \item{scr}{If \code{scr = TRUE}, the lossy screening rule is applied to preselect the neighborhood before the graph estimation. The default value is \code{FALSE}. NOT applicable when \code{method = "ct"}, {"mb"}, or {"tiger"}.} | ^ checkRd: (-1) huge.Rd:31: Lost braces; missing escapes or markup? 31 | \item{scr}{If \code{scr = TRUE}, the lossy screening rule is applied to preselect the neighborhood before the graph estimation. The default value is \code{FALSE}. NOT applicable when \code{method = "ct"}, {"mb"}, or {"tiger"}.} | ^ checkRd: (-1) huge.Rd:37: Lost braces; missing escapes or markup? 37 | \item{sym}{Symmetrize the output graphs. If \code{sym = "and"}, the edge between node \code{i} and node \code{j} is selected ONLY when both node \code{i} and node \code{j} are selected as neighbors for each other. If \code{sym = "or"}, the edge is selected when either node \code{i} or node \code{j} is selected as the neighbor for each other. The default value is \code{"or"}. ONLY applicable when \code{method = "mb"} or {"tiger"}.} | ^ checkRd: (-1) huge.glasso.Rd:26: Lost braces; missing escapes or markup? 26 | \item{scr}{If \code{scr = TRUE}, the lossy screening rule is applied to preselect the neighborhood before the graph estimation. The default value is \code{FALSE}. NOT applicable when \code{method = "ct"}, {"mb"}, or {"tiger"}.} | ^ checkRd: (-1) huge.glasso.Rd:26: Lost braces; missing escapes or markup? 26 | \item{scr}{If \code{scr = TRUE}, the lossy screening rule is applied to preselect the neighborhood before the graph estimation. The default value is \code{FALSE}. NOT applicable when \code{method = "ct"}, {"mb"}, or {"tiger"}.} | ^ checkRd: (-1) huge.mb.Rd:28: Lost braces; missing escapes or markup? 28 | \item{scr}{If \code{scr = TRUE}, the lossy screening rule is applied to preselect the neighborhood before the graph estimation. The default value is \code{FALSE}. NOT applicable when \code{method = "ct"}, {"mb"}, or {"tiger"}.} | ^ checkRd: (-1) huge.mb.Rd:28: Lost braces; missing escapes or markup? 28 | \item{scr}{If \code{scr = TRUE}, the lossy screening rule is applied to preselect the neighborhood before the graph estimation. The default value is \code{FALSE}. NOT applicable when \code{method = "ct"}, {"mb"}, or {"tiger"}.} | ^ checkRd: (-1) huge.mb.Rd:34: Lost braces; missing escapes or markup? 34 | \item{sym}{Symmetrize the output graphs. If \code{sym = "and"}, the edge between node \code{i} and node \code{j} is selected ONLY when both node \code{i} and node \code{j} are selected as neighbors for each other. If \code{sym = "or"}, the edge is selected when either node \code{i} or node \code{j} is selected as the neighbor for each other. The default value is \code{"or"}. ONLY applicable when \code{method = "mb"} or {"tiger"}.} | ^ checkRd: (-1) huge.tiger.Rd:25: Lost braces; missing escapes or markup? 25 | \item{sym}{Symmetrize the output graphs. If \code{sym = "and"}, the edge between node \code{i} and node \code{j} is selected ONLY when both node \code{i} and node \code{j} are selected as neighbors for each other. If \code{sym = "or"}, the edge is selected when either node \code{i} or node \code{j} is selected as the neighbor for each other. The default value is \code{"or"}. ONLY applicable when \code{method = "mb"} or {"tiger"}.} | ^ * 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 data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [47s/64s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [16s/22s] OK Running ‘test.R’ [16s/21s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [10s/14s] 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 NOTEs