• using R Under development (unstable) (2026-02-03 r89372)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-02-03 12:00:34Z
• using option ‘--no-stop-on-test-error’
• checking for file ‘gaiah/DESCRIPTION’ ... OK
• this is package ‘gaiah’ version ‘0.0.5’
• package encoding: UTF-8
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• checking whether package ‘gaiah’ can be installed ... [8s/21s] OK See the install log for details.
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• checking Rd files ... NOTE checkRd: (-1) min_hpd_inc_area_df.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) min_hpd_inc_area_df.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) min_hpd_inc_area_df.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces     20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as        | ^ checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces; missing escapes or markup?     20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as        | ^ checkRd: (-1) vza_mean_and_var_rasters.Rd:21: Lost braces; missing escapes or markup?     21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component        | ^
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• checking examples ... [22s/37s] ERROR Running examples in ‘gaiah-Ex.R’ failed The error most likely occurred in: > ### Name: comboize_and_fortify > ### Title: prepare fortified output for multipanel plot > ### Aliases: comboize_and_fortify > > ### ** Examples > > # run through the example for comboize to get the variables > # mgen, miso, and mhab that we will use. > example(comboize) comboz> # first, run through the example for isotope_posterior_probs() to get comboz> # the rasters for two migrant birds. This gives us the list "birds2" comboz> example(isotope_posterior_probs) istp__> # obtain posterior probability rasters for the first 2 birds in the migrant_wiwa_isotopes istp__> # data set. This takes about 15 seconds on my laptop (most of that time is preparatory---once istp__> # that is done, each bird goes much faster). So we don't run it here. istp__> ## Not run: istp__> ##D birds2 <- isotope_posterior_probs(isoscape = isomap_job54152_prediction, istp__> ##D ref_birds = breeding_wiwa_isotopes, istp__> ##D assign_birds = migrant_wiwa_isotopes[1:2,] istp__> ##D ) istp__> ## End(Not run) istp__> istp__> # However, you can load the results as a saved data object to see what they look like: istp__> birds2 <- example_isotope_posteriors istp__> # Since the ref_birds above were separate from the migrant birds, no leave-one-out was istp__> # performed. Hence birds2$loo_results is NULL, and all the results are in istp__> # birds2$regular. istp__> istp__> # Look at the names of the resulting output for the first bird: istp__> names(birds2$regular[[1]]) [1] "posterior_probs" "assignment_parameters" istp__> names(birds2$regular[[1]]$assignment_parameters) [1] "Tilde_T_mu" "R_sigma_squared" "a_bar" "b_bar" [5] "sd_indiv" istp__> # If you want to do self-assignment for a whole bunch of reference birds, it takes much longer. istp__> # It looks like this: istp__> ## Not run: istp__> ##D self_ass <- isotope_posterior_probs(isoscape = isomap_job54152_prediction, istp__> ##D ref_birds = breeding_wiwa_isotopes, istp__> ##D self_assign = TRUE) istp__> ## End(Not run) istp__> istp__> istp__> comboz> # extract the posterior probs rasters from that output into a raster stack comboz> miso <- lapply(birds2$regular, function(x) x$posterior_probs) %>% comboz+ raster::stack() comboz> # see the names of the birds we are dealing with: comboz> names(miso) [1] "WIWA02" "WIWA03" comboz> # get the genetic posteriors for those two birds comboz> mig_gen2 <- migrant_wiwa_genetic_posteriors %>% comboz+ dplyr::filter(ID %in% c(names(miso))) comboz> # make genetic posterior rasters for those two birds, make sure they are comboz> # sorted in the same order as miso, and make a raster stack of it comboz> mgen <- genetic_posteriors2rasters(G = mig_gen2, R = genetic_regions)[names(miso)] %>% comboz+ raster::stack() comboz> # make a normalized prior from habitat quality that is zeros everywhere comboz> # outside of the "known" range. comboz> tmp <- wiwa_habitat_unclipped * wiwa_breed comboz> mhab <- tmp / raster::cellStats(tmp, sum) comboz> # combine genetics, isotopes and habitat with exponents of 1 on each comboz> mcombo <- comboize(mgen, miso, mhab, 1, 1, 1) > > # then run that on the first bird to get a data frame > # that you can use with ggplot > ff <- comboize_and_fortify(mgen[[1]], miso[[1]], mhab) Error: ! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `tibble::as_tibble()` instead. Backtrace:      ▆   1. ├─gaiah::comboize_and_fortify(mgen[[1]], miso[[1]], mhab)   2. │ ├─... %>% dplyr::bind_rows(.id = "genetics_beta")   3. │ └─base::lapply(...)   4. │ └─gaiah (local) FUN(X[[i]], ...)   5. │ ├─... %>% dplyr::bind_rows(.id = "isotope_beta")   6. │ └─base::lapply(...)   7. │ └─gaiah (local) FUN(X[[i]], ...)   8. │ ├─... %>% dplyr::bind_rows(.id = "habitat_beta")   9. │ └─base::lapply(...)  10. │ └─gaiah (local) FUN(X[[i]], ...)  11. │ └─... %>% dplyr::tbl_df()  12. ├─dplyr::bind_rows(., .id = "genetics_beta")  13. │ └─rlang::list2(...)  14. ├─dplyr::bind_rows(., .id = "isotope_beta")  15. │ └─rlang::list2(...)  16. ├─dplyr::bind_rows(., .id = "habitat_beta")  17. │ └─rlang::list2(...)  18. └─dplyr::tbl_df(.)  19. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()")  20. └─lifecycle:::deprecate_stop0(msg)  21. └─rlang::cnd_signal(...) Execution halted
• checking PDF version of manual ... [8s/22s] OK
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• DONE

Status: 1 ERROR, 1 NOTE