* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/oncomsm.Rcheck’
* 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
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oncomsm’ can be installed ... [88s/113s] OK
See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/oncomsm-00install.html' 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
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/3s] OK
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* checking loading without being on the library search path ... [2s/3s] OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
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* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
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* checking for unstated dependencies in examples ... OK
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* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* 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
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)
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.
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
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)
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.
Why Weibull transition times?
In oncomsm, 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 '
* elapsed time (check, wall clock): 5:42