* using log directory 'd:/RCompile/CRANincoming/R-devel/douconca.Rcheck' * using R Under development (unstable) (2024-09-23 r87189 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'douconca/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'douconca' version '1.2.1' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [13s] INFO Maintainer: 'Bart-Jan van Rossum ' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'douconca' can be installed ... OK * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [12s] OK * checking Rd files ... OK * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'douconca-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getPlotdata > ### Title: Utility function: extracting data from a 'dc_CA' object for > ### plotting a single axis by your own code or 'plot.dcca'. > ### Aliases: getPlotdata > > ### ** Examples > > data("dune_trait_env") > > # rownames are carried forward in results > rownames(dune_trait_env$comm) <- dune_trait_env$comm$Sites > > # must delete "Sites" from response matrix or data frame > Y <- dune_trait_env$comm[, -1] # must delete "Sites" > > out <- dc_CA(formulaEnv = ~ A1 + Moist + Use + Manure + Mag, + formulaTraits = ~ SLA + Height + LDMC + Seedmass + Lifespan, + response = Y, + dataEnv = dune_trait_env$envir, + dataTraits = dune_trait_env$traits, + verbose = FALSE) > dat <- getPlotdata(out) > names(dat) [1] "CWM_SNC" "trait_env_scores" "newNameList" > names(dat$CWM_SNC) [1] "dcCA1" "score" "label" "CWM-SNC" [5] "weight" "type" "points" "sizeweight" [9] "smoothweight" "xforsmooth" "groups" "names" [13] "centroidnames" > levels(dat$CWM_SNC$groups) [1] "SF" "BF" "HF" "NM" "annual" "perennial" > > plot(out) Error in readRDS(nsInfoFilePath) : unknown input format Calls: plot ... plot.dcca -> plot_dcCA_CWM_SNC -> loadNamespace -> readRDS Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'tinytest.R' Running the tests in 'tests/tinytest.R' failed. Complete output: > if (requireNamespace("tinytest", quietly = TRUE)) { + tinytest::test_package("douconca") + } test_dcca.R................... 0 tests test_dcca.R................... 0 tests test_dcca.R................... 0 tests test_dcca.R................... 0 tests test_dcca.R................... 0 tests test_dcca.R................... 0 tests test_dcca.R................... 0 tests test_dcca.R................... 0 tests test_dcca.R................... 1 tests OK test_dcca.R................... 1 tests OK test_dcca.R................... 1 tests OK test_dcca.R................... 2 tests OK test_dcca.R................... 3 tests OK test_dcca.R................... 4 tests OK test_dcca.R................... 5 tests OK test_dcca.R................... 6 tests OK test_dcca.R................... 6 tests OK test_dcca.R................... 7 tests OK test_dcca.R................... 8 tests OK test_dcca.R................... 9 tests OK test_dcca.R................... 10 tests OK test_dcca.R................... 10 tests OK test_dcca.R................... 11 tests OK test_dcca.R................... 12 tests OK test_dcca.R................... 13 tests OK test_dcca.R................... 15 tests OK test_dcca.R................... 16 tests OK 0.5s test_fCWMSNC.R................ 0 tests test_fCWMSNC.R................ 0 tests test_fCWMSNC.R................ 0 tests test_fCWMSNC.R................ 0 tests test_fCWMSNC.R................ 0 tests test_fCWMSNC.R................ 1 tests OK test_fCWMSNC.R................ 2 tests OK test_fCWMSNC.R................ 2 tests OK test_fCWMSNC.R................ 3 tests OK test_fCWMSNC.R................ 4 tests OK test_fCWMSNC.R................ 4 tests OK test_fCWMSNC.R................ 4 tests OK test_fCWMSNC.R................ 4 tests OK test_fCWMSNC.R................ 4 tests OK test_fCWMSNC.R................ 5 tests OK test_fCWMSNC.R................ 6 tests OK test_fCWMSNC.R................ 7 tests OK test_fCWMSNC.R................ 8 tests OK test_fCWMSNC.R................ 8 tests OK test_fCWMSNC.R................ 8 tests OK test_fCWMSNC.R................ 9 tests OK test_fCWMSNC.R................ 10 tests OK test_fCWMSNC.R................ 10 tests OK test_fCWMSNC.R................ 10 tests OK test_fCWMSNC.R................ 10 tests OK test_fCWMSNC.R................ 10 tests OK test_fCWMSNC.R................ 11 tests OK test_fCWMSNC.R................ 12 tests OK test_fCWMSNC.R................ 12 tests OK test_fCWMSNC.R................ 12 tests OK test_fCWMSNC.R................ 13 tests OK 73ms test_plot.dcca.R.............. 0 tests test_plot.dcca.R.............. 0 tests test_plot.dcca.R.............. 0 tests test_plot.dcca.R.............. 0 tests test_plot.dcca.R.............. 0 tests test_plot.dcca.R.............. 1 tests OK Error in readRDS(nsInfoFilePath) : unknown input format Calls: ... plot.dcca -> plot_dcCA_CWM_SNC -> loadNamespace -> readRDS Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'douconca.Rmd' using rmarkdown Quitting from lines 171-172 [unnamed-chunk-5] (douconca.Rmd) Error: processing vignette 'douconca.Rmd' failed with diagnostics: unknown input format --- failed re-building 'douconca.Rmd' SUMMARY: processing the following file failed: 'douconca.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [18s] OK * checking HTML version of manual ... OK * DONE Status: 3 ERRORs