* using log directory ‘/srv/hornik/tmp/CRAN_pretest/darkroast.Rcheck’
* using R Under development (unstable) (2025-01-24 r87627)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘darkroast/DESCRIPTION’ ... OK
* this is package ‘darkroast’ version ‘1.0’
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Matthew Hofkes <mhofkes@mines.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  detrend (15:3)

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid file URI:
  URI: ..........
    From: inst/CITATION

The Date field is over a month old.

This build time stamp is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: ‘knitr’
* 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 ‘darkroast’ can be installed ... [4s/4s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Matthew Hofkes [aut, cre]’
  Authors@R: ‘Hofkes Matthew [aut, cre]’

Maintainer field differs from that derived from Authors@R
  Maintainer: ‘Matthew Hofkes <mhofkes@mines.edu>’
  Authors@R:  ‘Hofkes Matthew <mhofkes@mines.edu>’

* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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/7s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'BayesianSmoother2D.Rd':
  \usage lines wider than 90 characters:
         x1, x2, Y, covariates = FALSE, chain.length = 2000, burn.in = 1000, nugget.prior = "Weak",

Rd file 'HybridSmoother1D.Rd':
  \usage lines wider than 90 characters:
     HybridSmoother1D(x, y, lambda.grid, omega.grid, tolerance = 1e-4, initial.gamma.guess = rep(0, length(x) - 1), method = "AICc", constru ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BayesianSmoother2D.Rd: Tps, spatialProcess
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... NOTE
File 'data/datalist' is out-of-date:
  Data objects in 'datalist' not in 'data' directory:
    Headloss RoughSmoothSurface
  Data objects in 'data' directory not in 'datalist':
    anomalous.headloss.cycles regular.headloss.cycles X1.grid X2.grid Y
Please re-create using tools::add_datalist(force = TRUE).
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [116s/116s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
HybridBayesianSmoother2D 52.022  0.540  52.574
BayesianSmoother2D       34.585  0.195  34.786
ConvergenceCheck         25.230  0.112  25.350
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 6 NOTEs