* using log directory ‘/srv/hornik/tmp/CRAN_pretest/rLakeHabitat.Rcheck’ * using R Under development (unstable) (2025-03-23 r88038) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘rLakeHabitat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rLakeHabitat’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Tristan Blechinger ’ New submission Possibly misspelled words in DESCRIPTION: Bathymetry (3:20) DEMs (15:283) Secchi (15:474) bathymetric (15:34) epliminion (15:227) gstat (15:121) hypolimnion (15:252) metalimnion (15:239) photic (15:505) terra (15:131) thermocline (15:518) Found the following (possibly) invalid URLs: URL: https://gitlab.com/tblechin/rLakeHabitat From: DESCRIPTION Status: 403 Message: Forbidden URL: https://gitlab.com/tblechin/rLakeHabitat/issues From: DESCRIPTION Status: 403 Message: Forbidden The Description field should not start with the package name, 'This package' or similar. * 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 ‘rLakeHabitat’ can be installed ... [13s/13s] 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 ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [3s/3s] OK * checking loading without being on the library search path ... [4s/4s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘isoband’ Packages in Depends field not imported from: ‘dplyr’ ‘gstat’ ‘sf’ ‘terra’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [16s/16s] NOTE animBathy: no visible global function definition for ‘rast’ animBathy: no visible global function definition for ‘values’ animBathy: no visible binding for global variable ‘lyr1’ animBathy: no visible binding for global variable ‘wlf’ animBathy: no visible global function definition for ‘as.polygons’ animBathy: no visible binding for global variable ‘x’ animBathy: no visible binding for global variable ‘y’ animBathy: no visible binding for global variable ‘depth’ bathyMap: no visible global function definition for ‘rast’ bathyMap: no visible global function definition for ‘values’ bathyMap: no visible global function definition for ‘as.polygons’ bathyMap: no visible binding for global variable ‘x’ bathyMap: no visible binding for global variable ‘y’ bathyMap: no visible binding for global variable ‘lyr1’ calcHyps: no visible global function definition for ‘rast’ calcHyps: no visible global function definition for ‘expanse’ calcHyps: no visible binding for global variable ‘depth’ calcLittoral: no visible global function definition for ‘rast’ calcLittoral: no visible global function definition for ‘values’ calcLittoral: no visible global function definition for ‘expanse’ calcLittoral: no visible binding for global variable ‘lit_area’ calcLittoral: no visible binding for global variable ‘tot_area’ calcSDI: no visible global function definition for ‘rast’ calcSDI: no visible global function definition for ‘values’ calcSDI: no visible global function definition for ‘expanse’ calcSDI: no visible global function definition for ‘classify’ calcSDI: no visible global function definition for ‘as.polygons’ calcSDI: no visible global function definition for ‘perim’ calcVolume: no visible global function definition for ‘rast’ calcVolume: no visible global function definition for ‘values’ calcVolume: no visible global function definition for ‘expanse’ calcVolume: no visible binding for global variable ‘depth’ calcVolume: no visible binding for global variable ‘tot_vol_m3’ calcVolume: no visible binding for global variable ‘epi_vol_m3’ calcVolume: no visible binding for global variable ‘hyp_vol_m3’ calcVolume: no visible binding for global variable ‘tot_vol_acft’ calcVolume: no visible binding for global variable ‘epi_vol_acft’ calcVolume: no visible binding for global variable ‘hyp_vol_acft’ calcVolume: no visible binding for global variable ‘perc_epi_tot’ calcVolume: no visible binding for global variable ‘met_vol_m3’ calcVolume: no visible binding for global variable ‘met_vol_acft’ contourPoints: no visible global function definition for ‘st_as_sf’ contourPoints: no visible global function definition for ‘vect’ contourPoints: no visible global function definition for ‘densify’ contourPoints: no visible global function definition for ‘as.points’ contourPoints: no visible global function definition for ‘geom’ crossValidate: no visible global function definition for ‘vect’ crossValidate: no visible global function definition for ‘case_when’ crossValidate: no visible binding for global variable ‘group’ crossValidate: no visible global function definition for ‘n’ crossValidate: no visible binding for global variable ‘fold’ crossValidate: no visible binding for global variable ‘.’ crossValidate: no visible binding for global variable ‘zpred’ estThermo: no visible global function definition for ‘all_of’ estThermo: no visible binding for global variable ‘Thermo’ estThermo: no visible global function definition for ‘sd’ estThermo: no visible binding for global variable ‘.’ estThermo: no visible binding for global variable ‘Site’ estThermo: no visible global function definition for ‘n’ estThermo: no visible binding for global variable ‘Date’ genStack: no visible global function definition for ‘gdal’ genStack: no visible global function definition for ‘rast’ genStack: no visible global function definition for ‘values’ genStack: no visible global function definition for ‘writeRaster’ interpBathy: no visible global function definition for ‘vect’ interpBathy: no visible global function definition for ‘crs’ interpBathy : get_res: no visible global function definition for ‘crs’ interpBathy : get_res : get_best_utm: no visible global function definition for ‘centroids’ interpBathy : get_res : get_best_utm: no visible global function definition for ‘crds’ interpBathy : get_res : get_best_utm: no visible global function definition for ‘crs’ interpBathy : get_res: no visible global function definition for ‘project’ interpBathy: no visible global function definition for ‘rast’ interpBathy: no visible global function definition for ‘ext’ interpBathy: no visible global function definition for ‘all_of’ interpBathy: no visible global function definition for ‘densify’ interpBathy: no visible global function definition for ‘as.points’ interpBathy: no visible global function definition for ‘geom’ interpBathy: no visible global function definition for ‘disagg’ interpBathy: no visible global function definition for ‘rasterize’ interpBathy: no visible global function definition for ‘mask’ interpBathy: no visible global function definition for ‘gstat’ interpBathy: no visible global function definition for ‘na.omit’ interpBathy: no visible global function definition for ‘init’ interpBathy: no visible global function definition for ‘cover’ interpBathy: no visible global function definition for ‘variogram’ interpBathy: no visible global function definition for ‘fit.variogram’ interpBathy: no visible global function definition for ‘vgm’ littoralVol: no visible global function definition for ‘rast’ littoralVol: no visible global function definition for ‘values’ littoralVol: no visible global function definition for ‘expanse’ littoralVol: no visible binding for global variable ‘tot_area’ littoralVol: no visible binding for global variable ‘lit_area’ littoralVol: no visible binding for global variable ‘pel_area’ littoralVol: no visible binding for global variable ‘depth’ littoralVol: no visible binding for global variable ‘tot_vol_m3’ littoralVol: no visible binding for global variable ‘lit_vol_m3’ littoralVol: no visible binding for global variable ‘pel_vol_m3’ littoralVol: no visible binding for global variable ‘tot_vol_acft’ littoralVol: no visible binding for global variable ‘lit_vol_acft’ littoralVol: no visible binding for global variable ‘pel_vol_acft’ littoralVol: no visible binding for global variable ‘perc_lit_tot’ rarify: no visible global function definition for ‘vect’ rarify : get_res: no visible global function definition for ‘crs’ rarify : get_res : get_best_utm: no visible global function definition for ‘centroids’ rarify : get_res : get_best_utm: no visible global function definition for ‘crds’ rarify : get_res : get_best_utm: no visible global function definition for ‘crs’ rarify : get_res: no visible global function definition for ‘project’ rarify: no visible global function definition for ‘rast’ rarify: no visible global function definition for ‘ext’ rarify: no visible global function definition for ‘disagg’ rarify: no visible global function definition for ‘crs’ rarify: no visible global function definition for ‘rasterize’ rarify: no visible global function definition for ‘mask’ trueSA: no visible global function definition for ‘rast’ trueSA: no visible global function definition for ‘values’ trueSA: no visible global function definition for ‘ext’ trueSA: no visible global function definition for ‘res’ trueSA: no visible global function definition for ‘terrain’ trueSA: no visible binding for global variable ‘lit_area’ trueSA: no visible binding for global variable ‘tot_area’ Undefined global functions or variables: . Date Site Thermo all_of as.points as.polygons case_when centroids classify cover crds crs densify depth disagg epi_vol_acft epi_vol_m3 expanse ext fit.variogram fold gdal geom group gstat hyp_vol_acft hyp_vol_m3 init lit_area lit_vol_acft lit_vol_m3 lyr1 mask met_vol_acft met_vol_m3 n na.omit pel_area pel_vol_acft pel_vol_m3 perc_epi_tot perc_lit_tot perim project rast rasterize res sd st_as_sf terrain tot_area tot_vol_acft tot_vol_m3 values variogram vect vgm wlf writeRaster x y zpred Consider adding importFrom("stats", "na.omit", "sd") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'crossValidate.Rd': \examples lines wider than 100 characters: crossValidate(outline, data, "x", "y", "z", zeros = F, separation = 10, k = 5, crsUnit = "dd", res = 50, method = "IDW", nmax = 4, idp ... [TRUNCATED] Rd file 'estThermo.Rd': \examples lines wider than 100 characters: estThermo(data = data, site = "site", date = "date", depth = "depth", temp = "temp", combine = "all") Rd file 'interpBathy.Rd': \examples lines wider than 100 characters: interpBathy(outline, data, "x", "y", "z", zeros = F, separation = 10, crsUnit = "dd", res = 5, method = "IDW", nmax = 4, idp = 2) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘example_depths’ ‘example_profile_data’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [4s/4s] ERROR Running examples in ‘rLakeHabitat-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: animBathy > ### Title: Generate Animated Plot > ### Aliases: animBathy > > ### ** Examples > > #load raster > DEM <- rast(".data/example_raster.tif") Warning in new_CppObject_xp(fields$.module, fields$.pointer, ...) : GDAL Error 4: .data/example_raster.tif: No such file or directory Error: [rast] file does not exist: .data/example_raster.tif Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [5s/5s] ERROR Running ‘testthat.R’ [5s/5s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(rLakeHabitat) Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: terra terra 1.8.29 Attaching package: 'terra' The following objects are masked from 'package:testthat': compare, describe Loading required package: gstat Loading required package: sf Linking to GEOS 3.13.1, GDAL 3.10.2, PROJ 9.5.1; sf_use_s2() is TRUE > > test_check("rLakeHabitat") [ FAIL 14 | WARN 14 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-animBathy.R:4:1'): (code run outside of `test_that()`) ───────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-animBathy.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-bathyMap.R:4:1'): (code run outside of `test_that()`) ────────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-bathyMap.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-calcHyps.R:4:1'): (code run outside of `test_that()`) ────────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-calcHyps.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-calcLittoral.R:4:1'): (code run outside of `test_that()`) ────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-calcLittoral.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-calcSDI.R:4:1'): (code run outside of `test_that()`) ─────────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-calcSDI.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-calcVolume.R:4:1'): (code run outside of `test_that()`) ──────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-calcVolume.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-contourPoints.R:5:1'): (code run outside of `test_that()`) ───── Error in `file(file, "rt")`: cannot open the connection Backtrace: ▆ 1. └─utils::read.csv("data/example_depths.csv") at test-contourPoints.R:5:1 2. └─utils::read.table(...) 3. └─base::file(file, "rt") ── Error ('test-crossValidate.R:5:1'): (code run outside of `test_that()`) ───── Error in `file(file, "rt")`: cannot open the connection Backtrace: ▆ 1. └─utils::read.csv("data/example_depths.csv") at test-crossValidate.R:5:1 2. └─utils::read.table(...) 3. └─base::file(file, "rt") ── Error ('test-estThermo.R:4:1'): (code run outside of `test_that()`) ───────── Error in `file(file, "rt")`: cannot open the connection Backtrace: ▆ 1. ├─read.csv("data/example_profile_data.csv") %>% ... at test-estThermo.R:4:1 2. ├─dplyr::mutate(., date = as.Date(date)) 3. └─utils::read.csv("data/example_profile_data.csv") 4. └─utils::read.table(...) 5. └─base::file(file, "rt") ── Error ('test-genStack.R:4:1'): (code run outside of `test_that()`) ────────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-genStack.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-interpBathy.R:5:1'): (code run outside of `test_that()`) ─────── Error in `file(file, "rt")`: cannot open the connection Backtrace: ▆ 1. └─utils::read.csv("data/example_depths.csv") at test-interpBathy.R:5:1 2. └─utils::read.table(...) 3. └─base::file(file, "rt") ── Error ('test-littoralVol.R:4:1'): (code run outside of `test_that()`) ─────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-littoralVol.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) ── Error ('test-rarify.R:5:1'): (code run outside of `test_that()`) ──────────── Error in `file(file, "rt")`: cannot open the connection Backtrace: ▆ 1. └─utils::read.csv("data/example_depths.csv") at test-rarify.R:5:1 2. └─utils::read.table(...) 3. └─base::file(file, "rt") ── Error ('test-trueSA.R:4:1'): (code run outside of `test_that()`) ──────────── Error: [rast] file does not exist: inst/extdata/example_raster.tif Backtrace: ▆ 1. ├─terra::rast("inst/extdata/example_raster.tif") at test-trueSA.R:4:1 2. └─terra::rast("inst/extdata/example_raster.tif") 3. └─terra (local) .local(x, ...) 4. └─terra:::messages(r, "rast") 5. └─terra:::error(f, x@pntr$getError()) [ FAIL 14 | WARN 14 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/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: 2 ERRORs, 2 WARNINGs, 3 NOTEs