Check results for 'oncomsm'

using R version 4.3.0 (2023-04-21)
using platform: x86_64-apple-darwin20 (64-bit)
R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8
checking for file ‘oncomsm/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘oncomsm’ version ‘0.1.4’
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
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checking for sufficient/correct file permissions ... OK
checking whether package ‘oncomsm’ can be installed ... [88s/113s] OK See the install log for details.
used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used SDK: ‘MacOSX11.3.sdk’
checking C++ specification ... OK Not all R platforms support C++17
checking installed package size ... NOTE installed size is 39.6Mb sub-directories of 1Mb or more: doc 1.1Mb libs 37.4Mb
checking package directory ... OK
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checking DESCRIPTION meta-information ... OK
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checking dependencies in R code ... OK
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checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [6s/9s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [49s/89s] OK Running ‘testthat.R’ [49s/89s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [1s/1s] NONE ‘avoiding-bias.Rmd’ using ‘UTF-8’... [0s/1s] OK ‘oncomsm.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘prior-choice.Rmd’ using ‘UTF-8’... [0s/0s] OK
checking re-building of vignette outputs ... [24s/53s] ERROR Error(s) in re-building vignettes: --- re-building ‘avoiding-bias.Rmd’ using rmarkdown Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed. 2023-07-10 21:36:22.865 R[8426:2287719072] XType: Using static font registry. Warning in file.info(x, extra_cols = FALSE) : expanded path length 3828 would be too long for <pre><code class="language-r">library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union library(tidyr) library(oncomsm) </code></pre> tl;dr: During interim looks, individuals might still be stable and thus ‘at risk’ of either progression or response. Especially when the respective follow-up times differ, or if there is a difference in median time to response and median time to progression, this might lead to bias in the analysis of the response probability. <pre><code class="language-r">mdl <- create_srpmodel( A = define_srp_prior( median_t_q05 = c(1, 4, 12), # shorter time to response than progression median_t_q95 = c(6, 8, 36), # essentially fixed shape: shape_q05 = c(0.99, 0.99, 0.9 [... truncated] --- finished re-building ‘avoiding-bias.Rmd’ --- re-building ‘oncomsm.Rmd’ using rmarkdown Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed. Quitting from lines 52-58 [msm-1] (oncomsm.Rmd) Error: processing vignette 'oncomsm.Rmd' failed with diagnostics: Failed to start chrome. Error: --- failed re-building ‘oncomsm.Rmd’ --- re-building ‘prior-choice.Rmd’ using rmarkdown Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed. 2023-07-10 21:36:41.319 R[17427:2287737071] XType: Using static font registry. Warning in file.info(x, extra_cols = FALSE) : expanded path length 9231 would be too long for <pre><code class="language-r">library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union library(tidyr) library(ggplot2) library(oncomsm) </code></pre> tl;dr: Identification of the shape parameter is difficult settings with little data and it is thus recommended to restrict the shape parameter to $1$ (exponential model) if no historical data for the construction of an informative prior is available. A beta-mixture prior is suggested for the response probability and log-normal priors on shape and median time-to-next-event for the time-to-event components. <h2 id="why-weibull-transition-times">Why Weibull transition times?</h2> In <code>oncomsm</code>, the distributions of the between-state transition times [... truncated] --- finished re-building ‘prior-choice.Rmd’ SUMMARY: processing the following file failed: ‘oncomsm.Rmd’ Error: Vignette re-building failed. Execution halted
checking PDF version of manual ... [7s/12s] OK
DONE Status: 1 ERROR, 2 NOTEs
using check arguments '--no-clean-on-error '