* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/pharmr.Rcheck’ * using R Under development (unstable) (2024-04-22 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘pharmr/DESCRIPTION’ ... OK * this is package ‘pharmr’ version ‘0.96.0’ * 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 ‘pharmr’ can be installed ... [20s/22s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/pharmr-00install.html' for details. * checking package 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 ... [25s/27s] OK * checking Rd files ... NOTE checkRd: (-1) add_covariate_effect.Rd:44: Lost braces; missing escapes or markup? 44 | {coveff} = 1 + {theta} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:44: Lost braces; missing escapes or markup? 44 | {coveff} = 1 + {theta} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:44: Lost braces; missing escapes or markup? 44 | {coveff} = 1 + {theta} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:44: Lost braces; missing escapes or markup? 44 | {coveff} = 1 + {theta} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:60: Lost braces; missing escapes or markup? 60 | {coveff} = 1 | ^ checkRd: (-1) add_covariate_effect.Rd:67: Lost braces; missing escapes or markup? 67 | {coveff} = 1 + {theta} | ^ checkRd: (-1) add_covariate_effect.Rd:67: Lost braces; missing escapes or markup? 67 | {coveff} = 1 + {theta} | ^ checkRd: (-1) add_covariate_effect.Rd:79: Lost braces; missing escapes or markup? 79 | {coveff} = 1 + {theta1} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:79: Lost braces; missing escapes or markup? 79 | {coveff} = 1 + {theta1} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:79: Lost braces; missing escapes or markup? 79 | {coveff} = 1 + {theta1} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:79: Lost braces; missing escapes or markup? 79 | {coveff} = 1 + {theta1} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:86: Lost braces; missing escapes or markup? 86 | {coveff} = 1 + {theta2} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:86: Lost braces; missing escapes or markup? 86 | {coveff} = 1 + {theta2} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:86: Lost braces; missing escapes or markup? 86 | {coveff} = 1 + {theta2} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:86: Lost braces; missing escapes or markup? 86 | {coveff} = 1 + {theta2} * ({cov} - {median}) | ^ checkRd: (-1) add_covariate_effect.Rd:101: Lost braces; missing escapes or markup? 101 | {coveff} = exp({theta} * ({cov} - {median})) | ^ checkRd: (-1) add_covariate_effect.Rd:101: Lost braces; missing escapes or markup? 101 | {coveff} = exp({theta} * ({cov} - {median})) | ^ checkRd: (-1) add_covariate_effect.Rd:101: Lost braces; missing escapes or markup? 101 | {coveff} = exp({theta} * ({cov} - {median})) | ^ checkRd: (-1) add_covariate_effect.Rd:101: Lost braces; missing escapes or markup? 101 | {coveff} = exp({theta} * ({cov} - {median})) | ^ checkRd: (-1) add_covariate_effect.Rd:114: Lost braces 114 | min(frac{log(0.01)}{{min} - {median}}, | ^ checkRd: (-1) add_covariate_effect.Rd:114: Lost braces 114 | min(frac{log(0.01)}{{min} - {median}}, | ^ checkRd: (-1) add_covariate_effect.Rd:114: Lost braces; missing escapes or markup? 114 | min(frac{log(0.01)}{{min} - {median}}, | ^ checkRd: (-1) add_covariate_effect.Rd:115: Lost braces 115 | frac{log(100)}{{max} - {median}}) | ^ checkRd: (-1) add_covariate_effect.Rd:115: Lost braces 115 | frac{log(100)}{{max} - {median}}) | ^ checkRd: (-1) add_covariate_effect.Rd:115: Lost braces; missing escapes or markup? 115 | frac{log(100)}{{max} - {median}}) | ^ checkRd: (-1) add_covariate_effect.Rd:124: Lost braces 124 | max(frac{log(0.01)}{{max} - {median}}, | ^ checkRd: (-1) add_covariate_effect.Rd:124: Lost braces 124 | max(frac{log(0.01)}{{max} - {median}}, | ^ checkRd: (-1) add_covariate_effect.Rd:124: Lost braces; missing escapes or markup? 124 | max(frac{log(0.01)}{{max} - {median}}, | ^ checkRd: (-1) add_covariate_effect.Rd:125: Lost braces 125 | frac{log(100)}{{min} - {median}}) | ^ checkRd: (-1) add_covariate_effect.Rd:125: Lost braces 125 | frac{log(100)}{{min} - {median}}) | ^ checkRd: (-1) add_covariate_effect.Rd:125: Lost braces; missing escapes or markup? 125 | frac{log(100)}{{min} - {median}}) | ^ checkRd: (-1) add_covariate_effect.Rd:133: Lost braces; missing escapes or markup? 133 | {coveff} = (frac{{cov}}{{median}})^{theta} | ^ checkRd: (-1) add_covariate_effect.Rd:133: Lost braces 133 | {coveff} = (frac{{cov}}{{median}})^{theta} | ^ checkRd: (-1) add_covariate_effect.Rd:133: Lost braces 133 | {coveff} = (frac{{cov}}{{median}})^{theta} | ^ checkRd: (-1) add_covariate_effect.Rd:133: Lost braces; missing escapes or markup? 133 | {coveff} = (frac{{cov}}{{median}})^{theta} | ^ * 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 installed files from ‘inst/doc’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... OK Running ‘testthat.R’ * checking PDF version of manual ... [21s/25s] OK * checking HTML version of manual ... [8s/17s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE