* using log directory ‘/srv/hornik/tmp/CRAN_pretest/emln.Rcheck’ * using R Under development (unstable) (2026-04-19 r89916) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (3+b1) Debian flang version 21.1.8 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-04-20 09:36:06 UTC * checking for file ‘emln/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘emln’ version ‘1.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Geut Galai ’ New submission Possibly misspelled words in DESCRIPTION: ISF (16:364) Pilosof (16:412) Shai (16:407) multilayer (3:62, 16:63, 16:192, 16:293) Found the following (possibly) invalid URLs: URL: https://github.com/Ecological-Complexity-Lab/emln_package/issues From: DESCRIPTION man/emln-package.Rd Status: 404 Message: Not Found URL: https://github.com/ecomplab/emln/issues From: man/multilayer_to_csv.Rd man/multilayer_to_json.Rd man/plot_multilayer.Rd Status: 404 Message: Not Found The Title field should be in title case. Current version is: ‘A package to organize, handle, and explore ecological multilayer networks’ In title case that is: ‘A Package to Organize, Handle, and Explore Ecological Multilayer Networks’ * 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 ‘emln’ can be installed ... [10s/10s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [7s/7s] NOTE create_monolayer_network: no visible binding for global variable ‘name’ create_multilayer_network: no visible binding for global variable ‘layer’ create_multilayer_network: no visible binding for global variable ‘from’ create_multilayer_network: no visible binding for global variable ‘to’ load_emln: no visible binding for global variable ‘descriptions’ load_emln: no visible binding for global variable ‘layer’ load_emln: no visible binding for global variable ‘layer_id’ search_emln: no visible binding for global variable ‘descriptions’ view_emln: no visible binding for global variable ‘descriptions’ Undefined global functions or variables: descriptions from layer layer_id name to * checking Rd files ... [0s/0s] NOTE checkRd: (-1) descriptions.Rd:17: Lost braces; missing escapes or markup? 17 | @source {create} | ^ * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'get_sam.Rd': \examples lines wider than 100 characters: #https://ecological-complexity-lab.github.io/emln_package/multilayer.html#To_supra-adjacency_matrices These lines will be truncated in the PDF manual. * 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 ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [3s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [9s/9s] ERROR Running ‘testthat.R’ [8s/8s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(emln) > > test_check("emln") Input: a bipartite matrix Input: an unipartite edge list Input: a bipartite edge list Input: an igraph object: 3TRUEc(0, 1)c(1, 2)NULLNULLNULLNULLlist(c(1, 0, 1), list(), list(name = c("A", "B", "C")), list(weight = c(1, 1))) Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Input: a bipartite matrix Done. Layer #2 processing. Input: a bipartite matrix Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Input: a bipartite matrix Done. Layer #2 processing. Input: a bipartite matrix Done. Creating extended link list with node IDs Organizing state nodes Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, node_id)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, node_id)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, node_id)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, node_id)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, node_id)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, node_id)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, node_id)` Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Done. Layer #2 processing. Done. Creating extended link list with node IDs Organizing state nodes Layer attributes not provided, I added them (see layer_attributes in the final object) Layer #1 processing. Input: a bipartite matrix Done. Layer #2 processing. Input: a bipartite matrix Done. Creating extended link list with node IDs Organizing state nodes Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, layer_name)` Joining with `by = join_by(node_name, layer_name)` Warning: One or more rows sum to 0. This may be ok if you expect some links with only outgoing links (e.g., basal species in a food web) Warning: One or more columns sum to 0. This may be ok if you expect some links with only incoming links (e.g., top predators in a food web) Joining with `by = join_by(node_name, layer_name)` Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Creating state node map Creating extended link list with node IDs Assigning missing row names Assigning missing column names Assigning missing row and column names Saving _problems/test-search_emln-60.R Saving _problems/test-search_emln-68.R [ FAIL 2 | WARN 0 | SKIP 0 | PASS 126 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-search_emln.R:60:3'): search_emln filters by layer_number_minimum ── Error in `dplyr::filter(., .data$layer_num >= attributes_entered[["layer_number_minimum"]])`: i In argument: `.data$layer_num >= attributes_entered[["layer_number_minimum"]]`. Caused by error in `.data$layer_num >= attributes_entered[["layer_number_minimum"]]`: ! comparison (>=) is not possible for language types Backtrace: ▆ 1. ├─emln::search_emln(layer_number_minimum = min_layers) at test-search_emln.R:60:3 2. │ └─desc %>% ... 3. ├─dplyr::filter(., .data$layer_num >= attributes_entered[["layer_number_minimum"]]) 4. ├─dplyr:::filter.data.frame(., .data$layer_num >= attributes_entered[["layer_number_minimum"]]) 5. │ └─dplyr:::filter_impl(...) 6. │ └─dplyr:::filter_rows(...) 7. │ └─dplyr:::filter_eval(...) 8. │ ├─base::withCallingHandlers(...) 9. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 10. │ └─dplyr (local) eval() 11. └─base::.handleSimpleError(...) 12. └─dplyr (local) h(simpleError(msg, call)) 13. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-search_emln.R:68:3'): search_emln filters by node_number_minimum ── Error in `dplyr::filter(., .data$node_num >= attributes_entered[["node_number_minimum"]])`: i In argument: `.data$node_num >= attributes_entered[["node_number_minimum"]]`. Caused by error in `.data$node_num >= attributes_entered[["node_number_minimum"]]`: ! comparison (>=) is not possible for language types Backtrace: ▆ 1. ├─emln::search_emln(node_number_minimum = min_nodes) at test-search_emln.R:68:3 2. │ └─desc %>% ... 3. ├─dplyr::filter(., .data$node_num >= attributes_entered[["node_number_minimum"]]) 4. ├─dplyr:::filter.data.frame(., .data$node_num >= attributes_entered[["node_number_minimum"]]) 5. │ └─dplyr:::filter_impl(...) 6. │ └─dplyr:::filter_rows(...) 7. │ └─dplyr:::filter_eval(...) 8. │ ├─base::withCallingHandlers(...) 9. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter) 10. │ └─dplyr (local) eval() 11. └─base::.handleSimpleError(...) 12. └─dplyr (local) h(simpleError(msg, call)) 13. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 126 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 NOTEs