Local checks on MacOS fail, despite functions running fine in R console
bschilder opened this issue · comments
─ Test failures ─────────────────────── testthat ────
> desc_path <- list.files("../","^DESCRIPTION$",
+ full.names = TRUE, recursive = TRUE)[1]
> pkg <- read.dcf(desc_path, fields = "Package")[1]
> library(testthat)
> library(pkg, character.only = TRUE)
>
> test_check(pkg)
Loading required namespace: pkgnet
Generating `pkgnet` package report.
INFO [2022-11-12 03:01:52] Creating package report for package echolocatoR with reporters: SummaryReporter, DependencyReporter, FunctionReporter
INFO [2022-11-12 03:01:53] Rendering package report...
INFO [2022-11-12 03:02:05] Done creating package report! It is available at /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//Rtmpv6Wp7q/working_dir/RtmpkJtSMV/echolocatoR8345953adf3.html
Constructing dependency subgraph.
Adding all echoverse modules to metadata search.
Collecting metadata for 13 packages
- echolocatoR
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
echodeps
--- call from context ---
doTryCatch(return(expr), name, parentenv, handler)
--- call from argument ---
!methods::is(d, "data.frame") && is.na(d)
--- R stacktrace ---
where 1: doTryCatch(return(expr), name, parentenv, handler)
where 2: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 3: tryCatchList(expr, classes, parentenv, handlers)
where 4: tryCatch({
messager("-", pkg, v = verbose)
d <- utils::packageDescription(pkg)
if (!methods::is(d, "data.frame") && is.na(d)) {
return(NULL)
}
data.table::data.table(t(`names<-`(lapply(fields, function(x) {
if (is.null(d[[x]])) return(NA)
parse_deps(d = d, field = x, split = if (x %in% c("Title",
"Description")) "______" else ",")
}), fields)))
}, error = function(e) {
warning(e)
NULL
})
where 5: FUN(X[[i]], ...)
where 6: lapply(pkgs, function(pkg) {
tryCatch({
messager("-", pkg, v = verbose)
d <- utils::packageDescription(pkg)
if (!methods::is(d, "data.frame") && is.na(d)) {
return(NULL)
}
data.table::data.table(t(`names<-`(lapply(fields, function(x) {
if (is.null(d[[x]])) return(NA)
parse_deps(d = d, field = x, split = if (x %in% c("Title",
"Description")) "______" else ",")
}), fields)))
}, error = function(e) {
warning(e)
NULL
})
})
where 7: data.table::rbindlist(lapply(pkgs, function(pkg) {
tryCatch({
messager("-", pkg, v = verbose)
d <- utils::packageDescription(pkg)
if (!methods::is(d, "data.frame") && is.na(d)) {
return(NULL)
}
data.table::data.table(t(`names<-`(lapply(fields, function(x) {
if (is.null(d[[x]])) return(NA)
parse_deps(d = d, field = x, split = if (x %in% c("Title",
"Description")) "______" else ",")
}), fields)))
}, error = function(e) {
warning(e)
NULL
})
}))
where 8: package_metadata(pkgs = c(pkg_name, deps))
where 9: dep_graph_create(pkg_name = pkg_name, deps = deps, verbose = verbose)
where 10 at test-dep_graph.R#13: echodeps::dep_graph()
where 11: eval(code, test_env)
where 12: eval(code, test_env)
where 13: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 14: doTryCatch(return(expr), name, parentenv, handler)
where 15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 16: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 19: tryCatchList(expr, classes, parentenv, handlers)
where 20: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 21: test_code(desc, code, env = parent.frame(), reporter = reporter)
where 22 at test-dep_graph.R#1: test_that("dep_graph works", {
run_tests <- function(res, pkg_name) {
testthat::expect_true(methods::is(res$plot, "visNetwork"))
testthat::expect_true(methods::is(res$metadata, "data.frame"))
testthat::expect_true(methods::is(res$graph, "igraph"))
testthat::expect_true(methods::is(res$subgraph, "igraph"))
testthat::expect_true(methods::is(res$pkgnet_report,
"PackageReport"))
testthat::expect_equal(res$pkg_name, pkg_name)
}
res <- echodeps::dep_graph()
run_tests(res = res, pkg_name = "echolocatoR")
res2 <- echodeps::dep_graph(pkg_name = "dplyr", shape = "hexagon",
layout = function(graph, pkg_name) {
visNetwork::visIgraphLayout(graph = graph, layout = "layout_nicely")
})
run_tests(res = res2, pkg_name = "dplyr")
})
where 23: eval(code, test_env)
where 24: eval(code, test_env)
where 25: withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error)
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 28: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
where 29: doTryCatch(return(expr), name, parentenv, handler)
where 30: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
names[nh], parentenv, handlers[[nh]])
where 31: tryCatchList(expr, classes, parentenv, handlers)
where 32: tryCatch(withCallingHandlers({
eval(code, test_env)
if (!handled && !is.null(test)) {
skip_empty()
}
}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
message = handle_message, error = handle_error), error = handle_fatal,
skip = function(e) {
})
where 33: test_code(NULL, exprs, env)
where 34: source_file(path, child_env(env), wrap = wrap)
where 35: FUN(X[[i]], ...)
where 36: lapply(test_paths, test_one_file, env = env, wrap = wrap)
where 37: doTryCatch(return(expr), name, parentenv, handler)
where 38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 39: tryCatchList(expr, classes, parentenv, handlers)
where 40: tryCatch(code, testthat_abort_reporter = function(cnd) {
cat(conditionMessage(cnd), "\n")
NULL
})
where 41: with_reporter(reporters$multi, lapply(test_paths, test_one_file,
env = env, wrap = wrap))
where 42: test_files_serial(test_dir = test_dir, test_package = test_package,
test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,
env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap, load_package = load_package)
where 43: test_files(test_dir = path, test_paths = test_paths, test_package = package,
reporter = reporter, load_helpers = load_helpers, env = env,
stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
wrap = wrap, load_package = load_package, parallel = parallel)
where 44: test_dir("testthat", package = package, reporter = reporter,
..., load_package = "installed")
where 45: test_check(pkg)
--- value of length: 21 type: logical ---
Package Type Title
FALSE FALSE FALSE
Version Authors@R Description
FALSE FALSE FALSE
License URL BugReports
FALSE FALSE FALSE
Encoding Depends biocViews
FALSE FALSE FALSE
Imports Suggests Remotes
FALSE FALSE FALSE
RoxygenNote VignetteBuilder Config/testthat/edition
FALSE FALSE FALSE
Author Maintainer Built
FALSE FALSE FALSE
--- function from context ---
function (expr, name, parentenv, handler)
{
.Internal(.addCondHands(name, list(handler), parentenv, environment(),
FALSE))
expr
}
<bytecode: 0x7fcf6f074ab8>
<environment: 0x7fcf7c4c23a0>
--- function search by body ---
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
session info
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] echolocatoR_2.0.3 echodeps_0.99.2 dplyr_1.0.10 data.table_1.14.4
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.58.0 GGally_2.1.2
[4] R.methodsS3_1.8.2 tidyr_1.2.1 echoLD_0.99.8
[7] ggplot2_3.4.0 bit64_4.0.5 knitr_1.40
[10] irlba_2.3.5.1 DelayedArray_0.24.0 R.utils_2.12.2
[13] rpart_4.1.19 AnnotationFilter_1.22.0 KEGGREST_1.38.0
[16] RCurl_1.98-1.9 generics_0.1.3 BiocGenerics_0.44.0
[19] GenomicFeatures_1.50.2 callr_3.7.3 lambda.r_1.2.4
[22] usethis_2.1.6 RSQLite_2.2.18 proxy_0.4-27
[25] bit_4.0.4 tzdb_0.3.0 xml2_1.3.3
[28] httpuv_1.6.6 SummarizedExperiment_1.28.0 assertthat_0.2.1
[31] viridis_0.6.2 xfun_0.34 hms_1.1.2
[34] jquerylib_0.1.4 evaluate_0.18 promises_1.2.0.1
[37] fansi_1.0.3 restfulr_0.0.15 progress_1.2.2
[40] dbplyr_2.2.1 readxl_1.4.1 Rgraphviz_2.42.0
[43] igraph_1.3.5 DBI_1.1.3 htmlwidgets_1.5.4
[46] futile.logger_1.4.3 reshape_0.8.9 downloadR_0.99.5
[49] stats4_4.2.1 purrr_0.3.5 ellipsis_0.3.2
[52] crosstalk_1.2.0 ggnewscale_0.4.8 backports_1.4.1
[55] deldir_1.0-6 biomaRt_2.54.0 MatrixGenerics_1.10.0
[58] vctrs_0.5.0 Biobase_2.58.0 ensembldb_2.22.0
[61] remotes_2.4.2 cachem_1.0.6 withr_2.5.0
[64] BSgenome_1.66.1 checkmate_2.1.0 GenomicAlignments_1.34.0
[67] prettyunits_1.1.1 cluster_2.1.4 ape_5.6-2
[70] dir.expiry_1.6.0 lazyeval_0.2.2 crayon_1.5.2
[73] basilisk.utils_1.10.0 crul_1.3 pkgconfig_2.0.3
[76] GenomeInfoDb_1.34.3 ProtGenerics_1.30.0 nlme_3.1-160
[79] pkgload_1.3.1 XGR_1.1.8 pals_1.7
[82] nnet_7.3-18 gitcreds_0.1.2 devtools_2.4.5
[85] rlang_1.0.6 lifecycle_1.0.3 miniUI_0.1.1.1
[88] filelock_1.0.2 httpcode_0.3.0 BiocFileCache_2.6.0
[91] rex_1.2.1 dichromat_2.0-0.1 echotabix_0.99.8
[94] cellranger_1.1.0 coloc_5.1.0.1 rprojroot_2.0.3
[97] matrixStats_0.62.0 graph_1.76.0 Matrix_1.5-3
[100] osfr_0.2.9 boot_1.3-28 base64enc_0.1-3
[103] processx_3.8.0 png_0.1-7 viridisLite_0.4.1
[106] rjson_0.2.21 rootSolve_1.8.2.3 bitops_1.0-7
[109] R.oo_1.25.0 visNetwork_2.1.2 ggnetwork_0.5.10
[112] Biostrings_2.66.0 blob_1.2.3 mixsqp_0.3-43
[115] stringr_1.4.1 echoplot_0.99.6 dnet_1.1.7
[118] jpeg_0.1-9 readr_2.1.3 S4Vectors_0.36.0
[121] echodata_0.99.16 scales_1.2.1 memoise_2.0.1
[124] magrittr_2.0.3 plyr_1.8.8 hexbin_1.28.2
[127] pkgnet_0.4.2 zlibbioc_1.44.0 compiler_4.2.1
[130] echoconda_0.99.8 BiocIO_1.8.0 catalogueR_1.0.0
[133] RColorBrewer_1.1-3 covr_3.6.1 Rsamtools_2.14.0
[136] cli_3.4.1 XVector_0.38.0 echoannot_0.99.10
[139] urlchecker_1.0.1 patchwork_1.1.2 ps_1.7.2
[142] htmlTable_2.4.1 Formula_1.2-4 formatR_1.12
[145] MASS_7.3-58.1 tidyselect_1.2.0 stringi_1.7.8
[148] yaml_2.3.6 supraHex_1.36.0 latticeExtra_0.6-30
[151] ggrepel_0.9.2 grid_4.2.1 sass_0.4.2
[154] VariantAnnotation_1.44.0 tools_4.2.1 lmom_2.9
[157] parallel_4.2.1 rstudioapi_0.14 foreign_0.8-83
[160] piggyback_0.1.4 gridExtra_2.3 gld_2.6.6
[163] snpStats_1.48.0 digest_0.6.30 BiocManager_1.30.19
[166] shiny_1.7.3 Rcpp_1.0.9 GenomicRanges_1.50.1
[169] later_1.3.0 OrganismDbi_1.40.0 httr_1.4.4
[172] AnnotationDbi_1.60.0 biovizBase_1.46.0 RCircos_1.2.2
[175] ggbio_1.46.0 colorspace_2.0-3 brio_1.1.3
[178] XML_3.99-0.12 fs_1.5.2 reticulate_1.26
[181] splines_4.2.1 IRanges_2.32.0 RBGL_1.74.0
[184] expm_0.999-6 gh_1.3.1 echofinemap_0.99.4
[187] basilisk_1.10.2 Exact_3.2 mapproj_1.2.9
[190] sessioninfo_1.2.2 xtable_1.8-4 jsonlite_1.8.3
[193] futile.options_1.0.1 echogithub_0.99.0 testthat_3.1.5
[196] susieR_0.12.27 R6_2.5.1 Hmisc_4.7-1
[199] profvis_0.3.7 pillar_1.8.1 htmltools_0.5.3
[202] mime_0.12 glue_1.6.2 fastmap_1.1.0
[205] DT_0.26 BiocParallel_1.32.1 class_7.3-20
[208] codetools_0.2-18 maps_3.4.1 pkgbuild_1.3.1
[211] mvtnorm_1.1-3 utf8_1.2.2 lattice_0.20-45
[214] bslib_0.4.1 tibble_3.1.8 curl_4.3.3
[217] DescTools_0.99.47 interp_1.1-3 zip_2.2.2
[220] openxlsx_4.2.5.1 survival_3.4-0 roxygen2_7.2.2
[223] rmarkdown_2.18 desc_1.4.2 munsell_0.5.0
[226] e1071_1.7-12 GenomeInfoDbData_1.2.9 reshape2_1.4.4
[229] gtable_0.3.1
``
</details>
This is due to testthat struggling to find DESCRIPTION files during testing. Commented out these tests for now.