* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tsdf.Rcheck’
* using R version 4.4.3 RC (2025-02-20 r87814)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 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
* 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 serialization versions ... OK
* checking whether package ‘tsdf’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/tsdf-00install.html' 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
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [7s/9s] OK
* checking Rd files ... [0s/1s] 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
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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.}
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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.}
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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.}
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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. }
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* 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 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/6s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 NOTEs