* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/SIMICO.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * 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 ‘SIMICO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SIMICO’ version ‘0.2.0’ * 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 ‘SIMICO’ can be installed ... [17s/24s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/SIMICO-00install.html' for details. * 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 ... [17s/17s] OK * checking Rd files ... NOTE checkRd: (-1) fd_term.Rd:4: Lost braces; missing escapes or markup? 4 | d/d_{theta_l} | ^ checkRd: (-1) gamma_fd.Rd:4: Lost braces; missing escapes or markup? 4 | d/d_{gamma_l} | ^ checkRd: (-1) gamma_off.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{gamma_l}d{gamma_m} | ^ checkRd: (-1) gamma_off.Rd:4: Lost braces 4 | d^2/d_{gamma_l}d{gamma_m} | ^ checkRd: (-1) gamma_off.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the [off-diagonal] Information matrix term for I_{gamma gamma} with respect to outcome l and outcome m. | ^ checkRd: (-1) gamma_on.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{gamma_l}d{gamma_l} | ^ checkRd: (-1) gamma_on.Rd:4: Lost braces 4 | d^2/d_{gamma_l}d{gamma_l} | ^ checkRd: (-1) gamma_on.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the [on-diagonal] Information matrix term for I_{gamma gamma} with respect to outcome l. | ^ checkRd: (-1) gammasigma.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{gamma_l}d{sigma^2} | ^ checkRd: (-1) gammasigma.Rd:4: Lost braces 4 | d^2/d_{gamma_l}d{sigma^2} | ^ checkRd: (-1) gammasigma.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the Information matrix term of I_{eta gamma} for one outcome of interest l. | ^ checkRd: (-1) gammatheta.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{gamma_k}d{theta_k} | ^ checkRd: (-1) gammatheta.Rd:4: Lost braces 4 | d^2/d_{gamma_k}d{theta_k} | ^ checkRd: (-1) gammatheta.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the Information matrix term of I_{eta gamma} for outcome k. | ^ checkRd: (-1) gammatheta_off.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{gamma_l}d{theta_m} | ^ checkRd: (-1) gammatheta_off.Rd:4: Lost braces 4 | d^2/d_{gamma_l}d{theta_m} | ^ checkRd: (-1) gammatheta_off.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the Information matrix term of I_{eta gamma} for outcomes l and m | ^ checkRd: (-1) haz_left.Rd:4: Lost braces; missing escapes or markup? 4 | H_{ik}(L_{ik}) | ^ checkRd: (-1) haz_left.Rd:4: Lost braces; missing escapes or markup? 4 | H_{ik}(L_{ik}) | ^ checkRd: (-1) haz_right.Rd:4: Lost braces; missing escapes or markup? 4 | H_{ik}(R_{ik}) | ^ checkRd: (-1) haz_right.Rd:4: Lost braces; missing escapes or markup? 4 | H_{ik}(R_{ik}) | ^ checkRd: (-1) sd_off.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{theta_k}d{sigma^2} | ^ checkRd: (-1) sd_off.Rd:4: Lost braces 4 | d^2/d_{theta_k}d{sigma^2} | ^ checkRd: (-1) sd_off.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the Information matrix term of I_{theta sigma^2} for outcomes l and m. | ^ checkRd: (-1) sd_on.Rd:4: Lost braces 4 | d^2/d{sigma^2}^2 | ^ checkRd: (-1) sd_on.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the Information matrix term of I_{sigma^2 sigma^2} for outcome l. | ^ checkRd: (-1) simico_out.Rd:17: Lost braces; missing escapes or markup? 17 | \item{Itt}{I_{theta theta} - Information matrix of theta.} | ^ checkRd: (-1) ss_fd.Rd:4: Lost braces; missing escapes or markup? 4 | d/d_{sigma^2} | ^ checkRd: (-1) ss_sd.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{sigma^2}^2 | ^ checkRd: (-1) st_off.Rd:4: Lost braces; missing escapes or markup? 4 | d^2/d_{theta_l}d{sigma^2} | ^ checkRd: (-1) st_off.Rd:4: Lost braces 4 | d^2/d_{theta_l}d{sigma^2} | ^ checkRd: (-1) st_off.Rd:7: Lost braces; missing escapes or markup? 7 | Calculates the Information matrix term of I_{eta theta} for one outcome of interest l. | ^ checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik}) | ^ checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik}) | ^ checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik}) | ^ checkRd: (-1) surv_diff.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(L_{ik}) - S_{ik}(R_{ik}) | ^ checkRd: (-1) surv_left.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(L_{ik}) | ^ checkRd: (-1) surv_left.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(L_{ik}) | ^ checkRd: (-1) surv_right.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(R_{ik}) | ^ checkRd: (-1) surv_right.Rd:4: Lost braces; missing escapes or markup? 4 | S_{ik}(R_{ik}) | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... [12s/12s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [257s/259s] 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 NOTE