* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/fido.Rcheck’ * using R Under development (unstable) (2024-04-19 r86451) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘fido/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fido’ version ‘1.0.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘MicrobeDS’ * 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 ‘fido’ can be installed ... [14m/19m] OK * used C++ compiler: ‘g++-13 (GCC) 13.2.0’ * 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 ... [34s/41s] OK * checking Rd files ... NOTE checkRd: (-1) maltipoo_fit.Rd:72: Lost braces; missing escapes or markup? 72 | Where A = (I_N + X * Gamma * X')^{-1}, K^{-1} = Xi is a (D-1)x(D-1) | ^ checkRd: (-1) maltipoo_fit.Rd:72: Lost braces; missing escapes or markup? 72 | Where A = (I_N + X * Gamma * X')^{-1}, K^{-1} = Xi is a (D-1)x(D-1) | ^ checkRd: (-1) maltipoo_fit.Rd:74: Lost braces; missing escapes or markup? 74 | e^{ell_i} is a scale for that variance component and Phi^{-1} is | ^ checkRd: (-1) maltipoo_fit.Rd:74: Lost braces; missing escapes or markup? 74 | e^{ell_i} is a scale for that variance component and Phi^{-1} is | ^ checkRd: (-1) optimMaltipooCollapsed.Rd:110: Lost braces; missing escapes or markup? 110 | Where A = (I_N + e^{ell_1}\\*X\\*U_1\\*X' + ... + e^{ell_P}\\*X\\*U_P\\*X' ), | ^ checkRd: (-1) optimMaltipooCollapsed.Rd:110: Lost braces; missing escapes or markup? 110 | Where A = (I_N + e^{ell_1}\\*X\\*U_1\\*X' + ... + e^{ell_P}\\*X\\*U_P\\*X' ), | ^ checkRd: (-1) optimPibbleCollapsed.Rd:45: Lost braces; missing escapes or markup? 45 | \item{AInv}{N x N precision matrix given by (I_N + X'\emph{Gamma}X)^{-1}} | ^ checkRd: (-1) optimPibbleCollapsed.Rd:123: Lost braces; missing escapes or markup? 123 | matrix, Gamma is a Q x Q covariance matrix, and Phi^{-1} is ALRInv_D | ^ checkRd: (-1) orthus_fit.Rd:72: Lost braces; missing escapes or markup? 72 | Where Gamma is a Q x Q covariance matrix, and Phi^{-1} is | ^ checkRd: (-1) pibble_fit.Rd:72: Lost braces; missing escapes or markup? 72 | Where Gamma is a Q x Q covariance matrix, and Phi^{-1} is | ^ checkRd: (-1) uncollapsePibble.Rd:66: Lost braces; missing escapes or markup? 66 | matrix, Gamma is a Q x Q covariance matrix, and Phi^{-1} is ALRInv_D | ^ * 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 line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [21s/23s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [39s/46s] [39s/47s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(fido) Attaching package: 'fido' The following objects are masked from 'package:stats': coef, predict The following objects are masked from 'package:base': as.list, print, summary > > #Sys.setenv(KMP_DUPLICATE_LIB_OK="TRUE") > test_check("fido") [1] 0.45103633 0.01668484 2.39856096 -1.34675894 0.05358721 -1.22568111 [7] -1.47102180 0.80571722 1.13323335 -1.21244438 1.13952541 -0.26399339 [13] -0.98139619 1.14064345 0.42274509 -0.14956405 -1.59729587 -0.30939830 [19] -0.91554630 -0.19012327 0.54074096 -0.35295268 -0.02259354 0.94333710 [25] 2.45928904 -0.20206469 0.22725627 0.05284891 0.13684854 0.18397181 [31] 0.44105919 1.87718105 -1.57625007 3.00793317 1.22977287 -0.30491043 [37] 0.43180732 -0.16083632 -0.97132373 0.08816415 -0.94495073 0.56943548 [43] -1.39689503 -0.99757511 -0.23139317 0.20472374 -0.91883393 -0.56232782 [49] 2.06804948 1.02103836 1.87354028 -0.82278368 1.40782330 -0.62676164 [55] -1.25872442 -1.28802361 0.13953398 0.77706641 0.33243885 0.55044094 [61] -1.23979588 -0.96169987 -2.28759760 0.13583043 -2.20201055 -1.88855377 [67] -1.88776529 -1.31605562 -0.28714165 0.40877979 -0.33565577 -0.49688890 [73] 0.25828000 0.61376854 0.14389908 -0.11879720 -0.57947130 0.44867577 [79] 2.07473543 0.84767538 0.09785507 -1.02165870 -1.08288499 -1.03215830 [85] 1.28278391 -0.28416491 0.35174159 -1.21362240 -0.30749095 1.26857665 [91] -1.00722899 1.33512201 -1.75774301 0.24260802 0.06427525 -0.41941154 [97] 0.32793093 -0.09735275 -0.97073501 -0.98553640 $data # A tibble: 16 × 9 Parameter coord covariate val .lower .upper .width .point .interval 1 Lambda clr_c1 x1 4.60 4.36 4.85 0.5 mean qi 2 Lambda clr_c1 x2 -1.48 -1.78 -1.18 0.5 mean qi 3 Lambda clr_c2 x1 -6.50 -7.05 -5.93 0.5 mean qi 4 Lambda clr_c2 x2 -0.0195 -0.480 0.433 0.5 mean qi 5 Lambda clr_c1 x1 4.60 4.12 5.08 0.8 mean qi 6 Lambda clr_c1 x2 -1.48 -2.07 -0.911 0.8 mean qi 7 Lambda clr_c2 x1 -6.50 -7.57 -5.43 0.8 mean qi 8 Lambda clr_c2 x2 -0.0195 -0.896 0.854 0.8 mean qi 9 Lambda clr_c1 x1 4.60 3.89 5.32 0.95 mean qi 10 Lambda clr_c1 x2 -1.48 -2.37 -0.568 0.95 mean qi 11 Lambda clr_c2 x1 -6.50 -8.23 -4.96 0.95 mean qi 12 Lambda clr_c2 x2 -0.0195 -1.36 1.35 0.95 mean qi 13 Lambda clr_c1 x1 4.60 3.59 5.61 0.99 mean qi 14 Lambda clr_c1 x2 -1.48 -2.82 -0.263 0.99 mean qi 15 Lambda clr_c2 x1 -6.50 -8.77 -4.41 0.99 mean qi 16 Lambda clr_c2 x2 -0.0195 -1.67 1.80 0.99 mean qi $layers $layers[[1]] geom_interval: orientation = NA, interval_size_range = c(1, 6), interval_size_domain = c(1, 6), arrow = NULL, na.rm = FALSE stat_identity: na.rm = FALSE position_identity $layers[[2]] geom_point: na.rm = FALSE stat_identity: na.rm = FALSE position_identity $scales add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list train_df: function transform_df: function 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"element_text" "element" $ legend.text.position : NULL $ legend.title :List of 11 ..$ family : NULL ..$ face : NULL ..$ colour : NULL ..$ size : NULL ..$ hjust : num 0 ..$ vjust : NULL ..$ angle : NULL ..$ lineheight : NULL ..$ margin : NULL ..$ debug : NULL ..$ inherit.blank: logi TRUE ..- attr(*, "class")= chr [1:2] "element_text" "element" $ legend.title.position : NULL $ legend.position : chr "right" $ legend.position.inside : NULL $ legend.direction : NULL $ legend.byrow : NULL $ legend.justification : chr "center" $ legend.justification.top : NULL $ legend.justification.bottom : NULL $ legend.justification.left : NULL $ legend.justification.right : NULL $ legend.justification.inside : NULL $ legend.location : NULL $ legend.box : NULL $ legend.box.just : NULL $ legend.box.margin : 'margin' num [1:4] 0cm 0cm 0cm 0cm ..- attr(*, "unit")= int 1 $ legend.box.background : list() ..- attr(*, "class")= chr [1:2] "element_blank" "element" $ legend.box.spacing : 'simpleUnit' num 11points ..- attr(*, "unit")= int 8 [list output truncated] - attr(*, "class")= chr [1:2] "theme" "gg" - attr(*, "complete")= logi TRUE - attr(*, "validate")= logi TRUE $coordinates aspect: function backtransform_range: function clip: on default: TRUE distance: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: $facet compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panels: function finish_data: function init_scales: function map_data: function params: list setup_data: function setup_params: function shrink: TRUE train_scales: function vars: function super: $plot_env $layout coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: $labels $labels$x [1] "Log-Ratio Value" $labels$y [1] "coord" $labels$xmin [1] ".lower" $labels$xmax [1] ".upper" attr(,"class") [1] "gg" "ggplot" [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-ilr.R:11:3'): clr plus summary works ─────────────────────────── Error in `library(phyloseq)`: there is no package called 'phyloseq' Backtrace: ▆ 1. └─base::library(phyloseq) at test-ilr.R:11:3 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [11s/14s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/data/gannet/ripley/R/packages/tests-Suggests/fido.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 22:26.46, 965.56 + 68.91