* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/SIMICO.Rcheck’
* using R Under development (unstable) (2025-02-15 r87725)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc2
flang version 20.1.0-rc2
* running under: Fedora Linux 40 (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 ... [20s/71s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/SIMICO-00install.html' for details.
* 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 ... [4s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/14s] OK
* checking whether the package can be unloaded cleanly ... [4s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/17s] OK
* checking loading without being on the library search path ... [5s/18s] 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 ... [30s/107s] 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 ... [22s/83s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [6m/23m] OK
* checking PDF version of manual ... [8s/26s] 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