Last updated on 2024-12-23 12:49:46 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| oncomsm | 1 | 7 | 5 |
Current CRAN status: ERROR: 1, NOTE: 7, OK: 5
Version: 0.1.4
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.1.4
Check: installed package size
Result: NOTE
installed size is 49.0Mb
sub-directories of 1Mb or more:
doc 1.1Mb
libs 46.8Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.1.4
Check: re-building of vignette outputs
Result: 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>
<p><strong>tl;dr:</strong> <em>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.</em></p>
<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>
<p><strong>tl;dr:</strong> <em>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.</em></p>
<h2 id="why-weibull-transition-times">Why Weibull transition times?</h2>
<p>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
Flavor: r-oldrel-macos-x86_64