• using R version 4.3.1 (2023-06-16 ucrt)
• using platform: x86_64-w64-mingw32 (64-bit)
• R was compiled by     gcc.exe (GCC) 12.2.0     GNU Fortran (GCC) 12.2.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'biosurvey/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'biosurvey' version '0.1.1'
• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'biosurvey' can be installed ... OK See the install log for details.
• checking installed package size ... OK
• 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 ... [13s] OK
• checking whether the package can be loaded with stated dependencies ... [13s] OK
• checking whether the package can be unloaded cleanly ... [13s] OK
• checking whether the namespace can be loaded with stated dependencies ... [13s] OK
• checking whether the namespace can be unloaded cleanly ... [13s] OK
• checking loading without being on the library search path ... [13s] 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 ... [40s] OK
• checking Rd files ... [2s] OK
• checking Rd metadata ... 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 ... [10s] 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 ... [25s] ERROR Running examples in 'biosurvey-Ex.R' failed The error most likely occurred in: > ### Name: grid_from_region > ### Title: Creates grid for a given geographic region > ### Aliases: grid_from_region > > ### ** Examples > > # Data > data("mx", package = "biosurvey") > > # Create grid from polygon > grid_reg <- grid_from_region(region = mx, cell_size = 100) Warning in sp::CRS("+init=epsg:4326") :   sf required for evolution_status==2L Warning in spTransform(xSP, CRSobj, ...) :   NULL target CRS comment, falling back to PROJ string Warning in spTransform(xSP, CRSobj, ...) : +init dropped in PROJ string Warning in is.projected(p4str) : Package sf not available proj_create: unrecognized format / unknown name Error in .spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args, :   target crs creation failed: Invalid PROJ string syntax Calls: grid_from_region ... spTransform -> .spTransform_Polygons -> .spTransform_Polygon Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [40s] ERROR   Running 'testthat.R' [39s] Running the tests in 'tests/testthat.R' failed. Complete output:   > library(testthat)   > library(biosurvey)   The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,   which was just loaded, will retire in October 2023.   Please refer to R-spatial evolution reports for details, especially   https://r-spatial.org/r/2023/05/15/evolution4.html.   It may be desirable to make the sf package available;   package maintainers should consider adding sf to Suggests:.   The sp package is now running under evolution status 2        (status 2 uses the sf package in place of rgdal)   Please note that rgdal will be retired during October 2023,   plan transition to sf/stars/terra functions using GDAL and PROJ   at your earliest convenience.   See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution   rgdal: version: 1.6-7, (SVN revision 1203)   Geospatial Data Abstraction Library extensions to R successfully loaded   Loaded GDAL runtime: GDAL 3.6.2, released 2023/01/02   Path to GDAL shared files: D:/RCompile/CRANpkg/lib/4.3/rgdal/gdal    GDAL does not use iconv for recoding strings.   GDAL binary built with GEOS: TRUE   Loaded PROJ runtime: Rel. 9.2.0, March 1st, 2023, [PJ_VERSION: 920]   Path to PROJ shared files: D:/RCompile/CRANpkg/lib/4.3/rgdal/proj   PROJ CDN enabled: FALSE   Linking to sp version:2.0-0   To mute warnings of possible GDAL/OSR exportToProj4() degradation,   use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.   rgeos version: 0.6-3, (SVN revision 696)    GEOS runtime version: 3.11.2-CAPI-1.17.2    Please note that rgeos will be retired during October 2023,   plan transition to sf or terra functions using GEOS at your earliest convenience.   See https://r-spatial.org/r/2023/05/15/evolution4.html for details.    GEOS using OverlayNG    Linking to sp version: 2.0-0    Polygon checking: TRUE      >   > test_check("biosurvey")   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name        |     | | 0%     |     |================== | 25%     |     |=================================== | 50%     |     |==================================================== | 75%     |     |======================================================================| 100%   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   proj_create: unrecognized format / unknown name   [ FAIL 10 | WARN 56 | SKIP 0 | PASS 208 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-grid_from_region.R:4:3'): SPDF grid was produced successfully ──   Error in `.spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args,       ii = ii, jj = i, use_ob_tran = use_ob_tran, coordOp = coordOp,       enforce_xy = enforce_xy, aoi = aoi)`: target crs creation failed: Invalid PROJ string syntax   Backtrace:       ▆    1. └─biosurvey::grid_from_region(mx, 200) at test-grid_from_region.R:4:2    2. ├─sp::spTransform(region, WGS84)    3. └─sp::spTransform(region, WGS84)    4. ├─sp::spTransform(xSP, CRSobj, ...)    5. └─rgdal (local) spTransform(xSP, CRSobj, ...)    6. └─rgdal:::.spTransform_Polygons(...)    7. └─rgdal:::.spTransform_Polygon(...)   ── Error ('test-grid_from_region.R:20:3'): Errors and messages gfr ─────────────   Error in `.spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args,       ii = ii, jj = i, use_ob_tran = use_ob_tran, coordOp = coordOp,       enforce_xy = enforce_xy, aoi = aoi)`: target crs creation failed: Invalid PROJ string syntax   Backtrace:        ▆     1. ├─testthat::expect_message(grid_from_region(mx, 1000, complete_cover = FALSE)) at test-grid_from_region.R:20:2     2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. └─biosurvey::grid_from_region(mx, 1000, complete_cover = FALSE)     7. ├─sp::spTransform(region, WGS84)     8. └─sp::spTransform(region, WGS84)     9. ├─sp::spTransform(xSP, CRSobj, ...)    10. └─rgdal (local) spTransform(xSP, CRSobj, ...)    11. └─rgdal:::.spTransform_Polygons(...)    12. └─rgdal:::.spTransform_Polygon(...)   ── Error ('test-helpers_spp_tables.R:30:3'): Correct spdf_2data ────────────────   Error in `.spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args,       ii = ii, jj = i, use_ob_tran = use_ob_tran, coordOp = coordOp,       enforce_xy = enforce_xy, aoi = aoi)`: target crs creation failed: Invalid PROJ string syntax   Backtrace:       ▆    1. └─biosurvey::grid_from_region(region = mx, cell_size = 200) at test-helpers_spp_tables.R:30:2    2. ├─sp::spTransform(region, WGS84)    3. └─sp::spTransform(region, WGS84)    4. ├─sp::spTransform(xSP, CRSobj, ...)    5. └─rgdal (local) spTransform(xSP, CRSobj, ...)    6. └─rgdal:::.spTransform_Polygons(...)    7. └─rgdal:::.spTransform_Polygon(...)   ── Error ('test-prepare_base_PAM.R:4:3'): Correct creation of base_PAM ─────────   Error in `.spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args,       ii = ii, jj = i, use_ob_tran = use_ob_tran, coordOp = coordOp,       enforce_xy = enforce_xy, aoi = aoi)`: target crs creation failed: Invalid PROJ string syntax   Backtrace:       ▆    1. └─biosurvey::prepare_base_PAM(...) at test-prepare_base_PAM.R:4:2    2. └─biosurvey::grid_from_region(...)    3. ├─sp::spTransform(region, WGS84)    4. └─sp::spTransform(region, WGS84)    5. ├─sp::spTransform(xSP, CRSobj, ...)    6. └─rgdal (local) spTransform(xSP, CRSobj, ...)    7. └─rgdal:::.spTransform_Polygons(...)    8. └─rgdal:::.spTransform_Polygon(...)   ── Error ('test-prepare_base_PAM.R:26:3'): Errors and messages base_PAM ────────   Error in `.spTransform_Polygon(input[[i]], to_args = to_args, from_args = from_args,       ii = ii, jj = i, use_ob_tran = use_ob_tran, coordOp = coordOp,       enforce_xy = enforce_xy, aoi = aoi)`: target crs creation failed: Invalid PROJ string syntax   Backtrace:        ▆     1. ├─testthat::expect_message(...) at test-prepare_base_PAM.R:26:2     2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. └─biosurvey::prepare_base_PAM(...)     7. └─biosurvey::grid_from_region(...)     8. ├─sp::spTransform(region, WGS84)     9. └─sp::spTransform(region, WGS84)    10. ├─sp::spTransform(xSP, CRSobj, ...)    11. └─rgdal (local) spTransform(xSP, CRSobj, ...)    12. └─rgdal:::.spTransform_Polygons(...)    13. └─rgdal:::.spTransform_Polygon(...)   ── Error ('test-preselected_dist_mask.R:6:3'): Correct creation of mask ────────   Error in `spTransform(xSP, CRSobj, ...)`: source crs creation failed: Invalid PROJ string syntax   Backtrace:       ▆    1. └─biosurvey::preselected_dist_mask(...) at test-preselected_dist_mask.R:6:2    2. └─biosurvey::point_thinning(...)    3. └─biosurvey::wgs84_2aed_laea(data, x_column, y_column, which = "ED")    4. ├─sp::spTransform(dat_s, prj)    5. └─sp::spTransform(dat_s, prj)    6. ├─sp::spTransform(xSP, CRSobj, ...)    7. └─rgdal (local) spTransform(xSP, CRSobj, ...)   ── Error ('test-selection_helpers.R:7:3'): Correct point_thinning ──────────────   Error in `spTransform(xSP, CRSobj, ...)`: source crs creation failed: Invalid PROJ string syntax   Backtrace:       ▆    1. └─biosurvey::point_thinning(...) at test-selection_helpers.R:7:2    2. └─biosurvey::wgs84_2aed_laea(data, x_column, y_column, which = "ED")    3. ├─sp::spTransform(dat_s, prj)    4. └─sp::spTransform(dat_s, prj)    5. ├─sp::spTransform(xSP, CRSobj, ...)    6. └─rgdal (local) spTransform(xSP, CRSobj, ...)   ── Error ('test-short_helpers.R:17:3'): Errors wgs84_2aed_laea ─────────────────   Error in `spTransform(xSP, CRSobj, ...)`: source crs creation failed: Invalid PROJ string syntax   Backtrace:       ▆    1. └─biosurvey::wgs84_2aed_laea(...) at test-short_helpers.R:17:2    2. ├─sp::spTransform(dat_s, prj)    3. └─sp::spTransform(dat_s, prj)    4. ├─sp::spTransform(xSP, CRSobj, ...)    5. └─rgdal (local) spTransform(xSP, CRSobj, ...)   ── Error ('test-uniformG_selection.R:4:3'): Correct G master_selection ─────────   Error in `spTransform(xSP, CRSobj, ...)`: source crs creation failed: Invalid PROJ string syntax   Backtrace:       ▆    1. └─biosurvey::uniformG_selection(...) at test-uniformG_selection.R:4:2    2. └─biosurvey::preselected_dist_mask(...)    3. └─biosurvey::point_thinning(...)    4. └─biosurvey::wgs84_2aed_laea(data, x_column, y_column, which = "ED")    5. ├─sp::spTransform(dat_s, prj)    6. └─sp::spTransform(dat_s, prj)    7. ├─sp::spTransform(xSP, CRSobj, ...)    8. └─rgdal (local) spTransform(xSP, CRSobj, ...)   ── Error ('test-uniformG_selection.R:28:3'): Errors and messages G selection ───   Error in `spTransform(xSP, CRSobj, ...)`: source crs creation failed: Invalid PROJ string syntax   Backtrace:        ▆     1. ├─testthat::expect_message(...) at test-uniformG_selection.R:28:2     2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. └─biosurvey::uniformG_selection(...)     7. └─biosurvey::preselected_dist_mask(...)     8. └─biosurvey::point_thinning(...)     9. └─biosurvey::wgs84_2aed_laea(data, x_column, y_column, which = "ED")    10. ├─sp::spTransform(dat_s, prj)    11. └─sp::spTransform(dat_s, prj)    12. ├─sp::spTransform(xSP, CRSobj, ...)    13. └─rgdal (local) spTransform(xSP, CRSobj, ...)      [ FAIL 10 | WARN 56 | SKIP 0 | PASS 208 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking re-building of vignette outputs ... [10s] OK
• checking PDF version of manual ... [21s] OK
• checking HTML version of manual ... [13s] OK
• DONE

Status: 2 ERRORs