* using log directory ‘/Users/ripley/R/packages/tests-devel/BioTIMEr.Rcheck’ * using R Under development (unstable) (2024-04-09 r86373) * using platform: aarch64-apple-darwin23.4.0 * R was compiled by Apple clang version 15.0.0 (clang-1500.3.9.4) GNU Fortran (GCC) 12.2.0 * running under: macOS Sonoma 14.4.1 * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘BioTIMEr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioTIMEr’ version ‘0.2.2’ * 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 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 ‘BioTIMEr’ can be installed ... OK * 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 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 ... OK * checking Rd files ... 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 ... 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [30s/16s] [30s/16s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [26s/26s] ERROR Error(s) in re-building vignettes: --- re-building ‘vignette1.Rmd’ using rmarkdown BTsubset_meta package:BioTIMEr R Documentation _B_i_o_T_I_M_E _s_u_b_s_e_t _m_e_t_a_d_a_t_a _D_e_s_c_r_i_p_t_i_o_n: A subset of the metadata from BioTIME _U_s_a_g_e: BTsubset_meta _F_o_r_m_a_t: ## `BTsubset_meta` A data frame with 12 rows and 25 columns: STUDY_ID BioTIME study unique identifier REALM Realm of study location, i.e. Marine CLIMATE Climate of study location, i.e. Temperate HABITAT Habitat of study location, i.e. Rivers PROTECTED_AREA binary variable indicating if the study is within a protected area BIOME_MAP Biome of study location (taken from the WWF biomes, i.e. Temperate broadleaf and mixed forests TAXA High level taxonomic identity of study species, i.e. Fish ORGANISMS More detailed information on taxonomy, i.e. woody plants TITLE Title of study as identified in original source AB_BIO A, B or AB to designate abundance only, biomass only or both DATA_POINTS Number of unique data points in study, e.g. 10 data points spanning 15 years = 10 START_YEAR first year of study END_YEAR last year of study CENT_LAT Central latitude taken from the convex hull around all study coordinates CENT_LONG Central longitude taken from the convex hull around all study coordinates NUMBER_OF_SPECIES Number of distinct species in study NUMBER_OF_SAMPLES Number of distinct samples in study NUMBER_LAT_LONG Number of distinct geographic coordinates in study TOTAL Total number of records in study GRAIN_SQ_KM Grain size in km2, i.e. size of forest plots AREA_SQ_KM total area of study in km2 DATE_STUDY_ADDED Date that the study was added to the database ABUNDANCE_TYPE Type of abundance, i.e. count BIOMASS_TYPE Type of biomass, i.e. weight SAMPLE_DESC concatenation of descriptors comprising the unique sampling event _S_o_u_r_c_e: BTsubset_data package:BioTIMEr R Documentation _B_i_o_T_I_M_E _s_u_b_s_e_t _D_e_s_c_r_i_p_t_i_o_n: A subset of data from BioTIME temporal surveys. _U_s_a_g_e: BTsubset_data _F_o_r_m_a_t: ## `BTsubset_data` A data frame with 81,084 rows and 17 columns: ID_ALL_RAW_DATA Unique BioTIME identifier for record ABUNDANCE Double representing the abundance for the record (see metadata for details of ABUNDANCE_TYPE BIOMASS Double representing the biomass for the record (see metadata for details of BIOMASS_TYPE ID_SPECIES Unique identifier linking to the species table SAMPLE_DESC Concatenation of variables comprising unique sampling event PLOT Name or identifier of plot field, only used for fixed plots such as forest quadrats LATITUDE Latitude of record LONGITUDE Longitude of record DEPTH Depth or elevation of record if available DAY Numerical day of record MONTH Numerical value of month for record, i.e. January=1 YEAR Year of record STUDY_ID BioTIME study unique identifier newID Validated species identifier key valid_name Highest taxonomic resolution of individual, preferred is genus and species resolution Level of resolution, i.e. 'species' represented by genus and species taxon Higher level taxonomic grouping, i.e. Fish _S_o_u_r_c_e: Vignettes with name or keyword or title matching 'BioTIMEr' using fuzzy matching: BioTIMEr::vignette1 Introduction to BioTIMEr Type 'vignette(PKG::FOO)' to inspect entries 'PKG::FOO'. Help files with alias or concept or title matching 'BioTIMEr' using fuzzy matching: BioTIMEr::BTsubset_data BioTIME subset BioTIMEr::BTsubset_meta BioTIME subset metadata BioTIMEr::BioTIMEr-package BioTIMEr: Tools to Use and Explore the 'BioTIME' Database Aliases: BioTIMEr, BioTIMEr-package BioTIMEr::getLinearRegressions Get Linear Regressions BioTIME BioTIMEr::gridding gridding BioTIME data BioTIMEr::plotSlopes Plot slopes BioTIME Aliases: themeBioTIME BioTIMEr::rarefysamples Rarefy BioTIME data Applies sample-based rarefaction to standardise the number of samples per year within a cell-level time series. BioTIMEr::resampling Rarefy BioTIME data to an equal number of samples per year BioTIMEr::scale_color_biotime Scale construction for ggplot use Aliases: scale_color_biotime, scale_colour_biotime, scale_fill_biotime Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for entries like 'PKG::FOO-TYPE'. Quitting from lines at lines 471-490 [trends8] (vignette1.Rmd) Error: processing vignette 'vignette1.Rmd' failed with diagnostics: Faceting variables must have at least one value. --- failed re-building ‘vignette1.Rmd’ SUMMARY: processing the following file failed: ‘vignette1.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/Users/ripley/R/packages/tests-devel/BioTIMEr.Rcheck/00check.log’ for details. 79.10 real 78.15 user 9.53 sys