• using R version 4.4.2 (2024-10-31)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-6) 14.2.0     GNU Fortran (Debian 14.2.0-6) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘tsdf/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘tsdf’ version ‘1.1-8’
• package encoding: UTF-8
• checking package namespace information ... OK
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• checking for sufficient/correct file permissions ... OK
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• checking whether package ‘tsdf’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
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• checking R files for syntax errors ... OK
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• checking R code for possible problems ... [7s/9s] OK
• checking Rd files ... [0s/0s] NOTE checkRd: (-1) dec.sim.Rd:33: Lost braces; missing escapes or markup?     33 | Assume there are $d$ dose levels to be studied. Denote the cumulative number of patients treated and cumulative number of DLTs at the current dose level are $n_i$ and $m_i$, respectively. $n_{max}$ is the maximum number of patients permitted to be treated at each dose level. The procedure is as follows        | ^ checkRd: (-1) dec.sim.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) dec.sim.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) dec.sim.Rd:36: Lost braces; missing escapes or markup?     36 | \item{Step 2 : }{If $n_i = n_{max}$, declare dose i as the MTD; otherwise, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1.}        | ^ checkRd: (-1) dec.sim.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) dec.sim.Rd:37: Lost braces; missing escapes or markup?     37 | \item{Step 3 : }{If the current dose level is the highest dose level, then: if n_i < n_max, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the current dose is not the lowest dose, then: if $n_{i-1} < n_{max}$, update $m_{i-1}$ and $n_{i-1}$ with additional cohort of patients and set the current dose level to be the next lower dose level, and go to Step 1; otherwise, stop the trial and declare the next lower dose level is the MTD; Additionally, if the decision is ``DU'', record this dose level as DU and never treat additional patients at the current dose level again.}        | ^ checkRd: (-1) dec.sim.Rd:37: Lost braces; missing escapes or markup?     37 | \item{Step 3 : }{If the current dose level is the highest dose level, then: if n_i < n_max, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the current dose is not the lowest dose, then: if $n_{i-1} < n_{max}$, update $m_{i-1}$ and $n_{i-1}$ with additional cohort of patients and set the current dose level to be the next lower dose level, and go to Step 1; otherwise, stop the trial and declare the next lower dose level is the MTD; Additionally, if the decision is ``DU'', record this dose level as DU and never treat additional patients at the current dose level again.}        | ^ checkRd: (-1) dec.sim.Rd:37: Lost braces; missing escapes or markup?     37 | \item{Step 3 : }{If the current dose level is the highest dose level, then: if n_i < n_max, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the current dose is not the lowest dose, then: if $n_{i-1} < n_{max}$, update $m_{i-1}$ and $n_{i-1}$ with additional cohort of patients and set the current dose level to be the next lower dose level, and go to Step 1; otherwise, stop the trial and declare the next lower dose level is the MTD; Additionally, if the decision is ``DU'', record this dose level as DU and never treat additional patients at the current dose level again.}        | ^ checkRd: (-1) dec.sim.Rd:37: Lost braces; missing escapes or markup?     37 | \item{Step 3 : }{If the current dose level is the highest dose level, then: if n_i < n_max, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the current dose is not the lowest dose, then: if $n_{i-1} < n_{max}$, update $m_{i-1}$ and $n_{i-1}$ with additional cohort of patients and set the current dose level to be the next lower dose level, and go to Step 1; otherwise, stop the trial and declare the next lower dose level is the MTD; Additionally, if the decision is ``DU'', record this dose level as DU and never treat additional patients at the current dose level again.}        | ^ checkRd: (-1) dec.sim.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) dec.sim.Rd:38: Lost braces; missing escapes or markup?     38 | \item{Step 4 : }{If the current dose level is the highest dose level, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the next higher dose level is of status DU, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to step 1; otherwise stop, the current dose level is MTD; Otherwise: if $n_{i+1} < n_{max}$, update $m_{i+1}$ and $n_{i+1}$ with additional cohort of patients, set the current dose level to be next higher dose level, and go to step 1; else, the current dose level is the MTD. }        | ^ checkRd: (-1) dec.sim.Rd:38: Lost braces; missing escapes or markup?     38 | \item{Step 4 : }{If the current dose level is the highest dose level, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the next higher dose level is of status DU, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to step 1; otherwise stop, the current dose level is MTD; Otherwise: if $n_{i+1} < n_{max}$, update $m_{i+1}$ and $n_{i+1}$ with additional cohort of patients, set the current dose level to be next higher dose level, and go to step 1; else, the current dose level is the MTD. }        | ^ checkRd: (-1) dec.sim.Rd:38: Lost braces; missing escapes or markup?     38 | \item{Step 4 : }{If the current dose level is the highest dose level, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the next higher dose level is of status DU, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to step 1; otherwise stop, the current dose level is MTD; Otherwise: if $n_{i+1} < n_{max}$, update $m_{i+1}$ and $n_{i+1}$ with additional cohort of patients, set the current dose level to be next higher dose level, and go to step 1; else, the current dose level is the MTD. }        | ^ checkRd: (-1) dec.sim.Rd:38: Lost braces; missing escapes or markup?     38 | \item{Step 4 : }{If the current dose level is the highest dose level, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the next higher dose level is of status DU, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to step 1; otherwise stop, the current dose level is MTD; Otherwise: if $n_{i+1} < n_{max}$, update $m_{i+1}$ and $n_{i+1}$ with additional cohort of patients, set the current dose level to be next higher dose level, and go to step 1; else, the current dose level is the MTD. }        | ^ checkRd: (-1) dec.sim.Rd:38: Lost braces; missing escapes or markup?     38 | \item{Step 4 : }{If the current dose level is the highest dose level, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the next higher dose level is of status DU, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to step 1; otherwise stop, the current dose level is MTD; Otherwise: if $n_{i+1} < n_{max}$, update $m_{i+1}$ and $n_{i+1}$ with additional cohort of patients, set the current dose level to be next higher dose level, and go to step 1; else, the current dose level is the MTD. }        | ^ checkRd: (-1) dec.sim.Rd:38: Lost braces; missing escapes or markup?     38 | \item{Step 4 : }{If the current dose level is the highest dose level, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to Step 1; otherwise, stop the trial and declare that the MTD is higher than the highest dose level (inconclusive); If the next higher dose level is of status DU, then: if $n_i < n_{max}$, update $m_i$ and $n_i$ with additional cohort of patients and go to step 1; otherwise stop, the current dose level is MTD; Otherwise: if $n_{i+1} < n_{max}$, update $m_{i+1}$ and $n_{i+1}$ with additional cohort of patients, set the current dose level to be next higher dose level, and go to step 1; else, the current dose level is the MTD. }        | ^
• checking Rd metadata ... OK
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• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking LazyData ... NOTE   'LazyData' is specified without a 'data' directory
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/5s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [0s/1s] OK
• checking PDF version of manual ... [4s/7s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 NOTEs