rajlabmssm / echodeps Goto Github PK
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Home Page: https://rajlabmssm.github.io/echodeps/
echoverse module: Create package dependency graphs
Home Page: https://rajlabmssm.github.io/echodeps/
This will be helpful for making the main echolocatoR
docs site more comprehensive.
deepdep
https://dominikrafacz.github.io/deepdep/
Great idea, but seems to be broken atm. Also doesn't seem to be able to find reverse depdencies.
Has a helpful pros/cons comparison with other similar packages:
https://dominikrafacz.github.io/deepdep/articles/deepdep-comparison.html
miniCRAN
Useful function for getting CRAN description files:
res <- miniCRAN::getCranDescription(pkgs = "miniCRAN")
Can then convert to desc
format :
dl <- as.list(res)
d <- desc::description$new("!new")
for(k in names(dl)){
if(!is.na(dl[[k]])){
d$set_list(key = k, list_value = dl[[k]])
}
}
However, it only has access to CRAN.
Moreover, it seems like it can only access INSTALLED CRAN packages....so not very useful.
BiocPkgTools
Package dependency graphs and download stats of Bioc packages. Recently updated
https://bioconductor.org/packages/release/bioc/vignettes/BiocPkgTools/inst/doc/BiocPkgTools.html
ALso has access to DESCRIPTION files:
bpi = biocPkgList()
Also has access to anacondaDownloadStats
, another repo I should consider incorporating into echodeps
for download stats.
Comes with tons of pre-parsed GitHub metadata for each package.
awesome-r-pkgtools
Repo documenting lots of awesome R dev tools, including dep management:
https://github.com/IndrajeetPatil/awesome-r-pkgtools#dependency-management-%EF%B8%8F
pkgdepends
https://r-lib.github.io/pkgdepends/
Not very useful for my case, since you have to download each R package and install it....
─ 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
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>
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