From 5c9d6bdc45e940af075690f3fe0181811e3977f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Tue, 24 Sep 2024 15:39:52 +0200 Subject: [PATCH 1/2] chore!: remove deprecated `neimode` parameter from `bfs` / `dfs`; originally planned for removal in 1.4.0 --- R/structural.properties.R | 10 ++-------- tests/testthat/_snaps/structural.properties.md | 8 ++++---- tests/testthat/test-structural.properties.R | 4 ++-- 3 files changed, 8 insertions(+), 14 deletions(-) diff --git a/R/structural.properties.R b/R/structural.properties.R index ca1029e1420..30cb7d930d9 100644 --- a/R/structural.properties.R +++ b/R/structural.properties.R @@ -2140,14 +2140,11 @@ bfs <- function( ensure_igraph(graph) if (lifecycle::is_present(neimode)) { - lifecycle::deprecate_warn( + lifecycle::deprecate_stop( "1.3.0", "bfs(neimode)", "bfs(mode)" ) - if (missing(mode)) { - mode <- neimode - } } if (length(root) == 1) { @@ -2315,14 +2312,11 @@ dfs <- function(graph, root, mode = c("out", "in", "all", "total"), rho = parent.frame(), neimode = deprecated()) { ensure_igraph(graph) if (lifecycle::is_present(neimode)) { - lifecycle::deprecate_warn( + lifecycle::deprecate_stop( "1.3.0", "dfs(neimode)", "dfs(mode)" ) - if (missing(mode)) { - mode <- neimode - } } root <- as_igraph_vs(graph, root) - 1 diff --git a/tests/testthat/_snaps/structural.properties.md b/tests/testthat/_snaps/structural.properties.md index d8f926aeba1..55f08216249 100644 --- a/tests/testthat/_snaps/structural.properties.md +++ b/tests/testthat/_snaps/structural.properties.md @@ -3,8 +3,8 @@ Code d <- dfs(g, root = 2, unreachable = FALSE, neimode = "out") Condition - Warning: - The `neimode` argument of `dfs()` is deprecated as of igraph 1.3.0. + Error: + ! The `neimode` argument of `dfs()` was deprecated in igraph 1.3.0 and is now defunct. i Please use the `mode` argument instead. --- @@ -13,8 +13,8 @@ b <- bfs(g, root = 2, neimode = "out", unreachable = FALSE, order = TRUE, rank = TRUE, father = TRUE, pred = TRUE, succ = TRUE, dist = TRUE) Condition - Warning: - The `neimode` argument of `bfs()` is deprecated as of igraph 1.3.0. + Error: + ! The `neimode` argument of `bfs()` was deprecated in igraph 1.3.0 and is now defunct. i Please use the `mode` argument instead. # bfs() works diff --git a/tests/testthat/test-structural.properties.R b/tests/testthat/test-structural.properties.R index 15089e98d3f..de12134cf12 100644 --- a/tests/testthat/test-structural.properties.R +++ b/tests/testthat/test-structural.properties.R @@ -15,7 +15,7 @@ test_that("dfs() does not pad order", { test_that("bfs() deprecated argument", { g <- make_star(3) - expect_snapshot({ + expect_snapshot(error = TRUE, { d <- dfs( g, root = 2, @@ -199,7 +199,7 @@ test_that("bfs() works", { test_that("bfs() deprecated argument", { g <- graph_from_literal(a - +b - +c, z - +a, d) - expect_snapshot({ + expect_snapshot(error = TRUE, { b <- bfs( g, root = 2, From 6ea56f897c7617cea5f9f8784d624d22647dd80d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Thu, 7 Nov 2024 15:21:16 +0100 Subject: [PATCH 2/2] Results --- revdep/README.md | 13 ++- revdep/cran.md | 19 ++-- revdep/problems.md | 245 +++++++++++++++++++++------------------------ 3 files changed, 127 insertions(+), 150 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index ff107590b45..862f93fb2f0 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -4,15 +4,14 @@ |package |version |error |warning |note | |:---------|:-------|:-----|:-------|:----| -|bnlearn |5.0.1 |1 | | | |datapack |1.4.1 |1 | | | +|multinma |0.7.2 |1 | | | |streamDAG |? | | | | -## New problems (3) +## New problems (2) -|package |version |error |warning |note | -|:---------|:-------|:------|:-------|:----| -|[manynet](problems.md#manynet)|1.2.6 |__+1__ | |3 | -|[simcausal](problems.md#simcausal)|0.5.6 |__+1__ |1 | | -|[skynet](problems.md#skynet)|1.4.3 |__+1__ | |1 | +|package |version |error |warning |note | +|:--------|:-------|:------|:-------|:----| +|[ssifs](problems.md#ssifs)|1.0.2 |__+2__ | | | +|[tilemaps](problems.md#tilemaps)|0.2.0 |__+2__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index d15a90e3e3e..ebebbfe07b9 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,8 +1,8 @@ ## revdepcheck results -We checked 7 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 868 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 3 new problems + * We saw 2 new problems * We failed to check 3 packages Issues with CRAN packages are summarised below. @@ -10,17 +10,16 @@ Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* manynet - checking tests ... ERROR +* ssifs + checking examples ... ERROR + checking re-building of vignette outputs ... ERROR -* simcausal - checking tests ... ERROR - -* skynet - checking tests ... ERROR +* tilemaps + checking examples ... ERROR + checking re-building of vignette outputs ... ERROR ### Failed to check -* bnlearn (NA) * datapack (NA) +* multinma (NA) * streamDAG (NA) diff --git a/revdep/problems.md b/revdep/problems.md index 4e4b620628b..4a3f4d7bb12 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,178 +1,157 @@ -# manynet +# ssifs
-* Version: 1.2.6 -* GitHub: https://github.com/stocnet/manynet -* Source code: https://github.com/cran/manynet -* Date/Publication: 2024-10-05 16:40:01 UTC -* Number of recursive dependencies: 146 +* Version: 1.0.2 +* GitHub: https://github.com/georgiosseitidis/ssifs +* Source code: https://github.com/cran/ssifs +* Date/Publication: 2023-05-12 09:00:03 UTC +* Number of recursive dependencies: 94 -Run `revdepcheck::cloud_details(, "manynet")` for more info +Run `revdepcheck::cloud_details(, "ssifs")` for more info
## Newly broken -* checking tests ... ERROR +* checking examples ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(manynet) - > - > test_check("manynet") - Starting 2 test processes - [ FAIL 7 | WARN 18643 | SKIP 21 | PASS 558 ] - - ... - `expected`: 0.2 0.1 0.1 - ── Failure ('test-measure_centrality.R:79:3'): two mode eigenvector centrality calculated correctly ── - top3(node_eigenvector(test_igr, normalized = TRUE)) (`actual`) not equal to c(0.4505, 0.4248, 0.5) (`expected`). - - `actual`: 1.3 1.2 1.4 - `expected`: 0.5 0.4 0.5 - - [ FAIL 7 | WARN 18643 | SKIP 21 | PASS 558 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘Rgraphviz’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - R 1.5Mb - tutorials 1.8Mb + Running examples in ‘ssifs-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Alcohol + > ### Title: Stochastic Search Inconsistency Factor Selection of brief + > ### alcohol interventions. + > ### Aliases: Alcohol + > + > ### ** Examples + > + > data(Alcohol) + > + > TE <- Alcohol$TE + > seTE <- Alcohol$seTE + > studlab <- Alcohol$studyid + > treat1 <- Alcohol$treat2 + > treat2 <- Alcohol$treat1 + > + > # Stochastic Search Inconsistency Factor Selection using as reference treatment AO-CT and the + > # design-by-treatment method for the specification of the Z matrix. + > + > m <- ssifs(TE, seTE, treat1, treat2, studlab, ref = "AO-CT", + + M = 1000, B = 100, M_pilot = 1000, B_pilot = 100) + Error: + ! The `neimode` argument of `dfs()` was deprecated in igraph 1.3.0 and + is now defunct. + ℹ Please use the `mode` argument instead. + Backtrace: + ▆ + 1. └─ssifs::ssifs(...) + 2. └─ssifs:::connet(data) + 3. └─ssifs:::subnet(data) + 4. ├─base::suppressWarnings(RevEcoR::KosarajuSCC(t)) + 5. │ └─base::withCallingHandlers(...) + 6. └─RevEcoR::KosarajuSCC(t) + 7. └─igraph::graph.dfs(g, root = Source.node, neimode = "out", unreachable = FALSE) + 8. └─igraph::dfs(...) + 9. └─lifecycle::deprecate_stop("1.3.0", "dfs(neimode)", "dfs(mode)") + 10. └─lifecycle:::deprecate_stop0(msg) + 11. └─rlang::cnd_signal(...) + Execution halted ``` -* checking data for non-ASCII characters ... NOTE +* checking re-building of vignette outputs ... ERROR ``` - Note: found 7 marked UTF-8 strings + Error(s) in re-building vignettes: + ... + --- re-building ‘An_introduction_to_ssifs.Rmd’ using rmarkdown + + Quitting from lines 133-135 [unnamed-chunk-4] (An_introduction_to_ssifs.Rmd) + Error: processing vignette 'An_introduction_to_ssifs.Rmd' failed with diagnostics: + The `neimode` argument of `dfs()` was deprecated in igraph 1.3.0 and is + now defunct. + ℹ Please use the `mode` argument instead. + --- failed re-building ‘An_introduction_to_ssifs.Rmd’ + + SUMMARY: processing the following file failed: + ‘An_introduction_to_ssifs.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -# simcausal +# tilemaps
-* Version: 0.5.6 -* GitHub: https://github.com/osofr/simcausal -* Source code: https://github.com/cran/simcausal -* Date/Publication: 2022-10-28 11:52:27 UTC -* Number of recursive dependencies: 83 +* Version: 0.2.0 +* GitHub: https://github.com/kaerosen/tilemaps +* Source code: https://github.com/cran/tilemaps +* Date/Publication: 2020-07-10 04:20:02 UTC +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "simcausal")` for more info +Run `revdepcheck::cloud_details(, "tilemaps")` for more info
## Newly broken -* checking tests ... ERROR +* checking examples ... ERROR ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Complete output: - > ## unit tests will not be done if RUnit is not available - > # setwd("..") - > # getwd() - > # library(RUnit) - > if(require("RUnit", quietly=TRUE)) { - + ## --- Setup --- - + - ... - ℹ Please use `as_directed()` instead. - 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : - RNGkind: Marsaglia-Multicarry has poor statistical properties - 3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : - RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry - 4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : - RNGkind: Marsaglia-Multicarry has poor statistical properties - 5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : - RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry - Execution halted + Running examples in ‘tilemaps-Ex.R’ failed + The error most likely occurred in: + + > ### Name: create_island + > ### Title: Create a Tile for an Island + > ### Aliases: create_island + > + > ### ** Examples + > + > library(sf) + Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE + > northeast <- governors[c(6,7,17,18,19,27,28,30,36,37,43),] + > tile_map <- generate_map(northeast$geometry, square = FALSE) + Error: + ! The `neimode` argument of `bfs()` was deprecated in igraph 1.3.0 and + is now defunct. + ℹ Please use the `mode` argument instead. + Backtrace: + ▆ + 1. └─tilemaps::generate_map(northeast$geometry, square = FALSE) + 2. └─igraph::bfs(neighbor_graph, 1, neimode = "all", unreachable = FALSE) + 3. └─lifecycle::deprecate_stop("1.3.0", "bfs(neimode)", "bfs(mode)") + 4. └─lifecycle:::deprecate_stop0(msg) + 5. └─rlang::cnd_signal(...) + Execution halted ``` -## In both - -* checking re-building of vignette outputs ... WARNING +* checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... - --- re-building ‘simcausal_vignette.Rnw’ using knitr - Error: processing vignette 'simcausal_vignette.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'simcausal_vignette.tex' failed. - LaTeX errors: - ! LaTeX Error: File `colortbl.sty' not found. + --- re-building ‘tilemaps.Rmd’ using rmarkdown - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.55 \RequirePackage - [T1]{fontenc}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘simcausal_vignette.Rnw’ + Quitting from lines 33-41 [unnamed-chunk-2] (tilemaps.Rmd) + Error: processing vignette 'tilemaps.Rmd' failed with diagnostics: + ℹ In argument: `tile_map = generate_map(geometry, square = FALSE, + flat_topped = TRUE)`. + Caused by error: + ! The `neimode` argument of `bfs()` was deprecated in igraph 1.3.0 and + is now defunct. + ℹ Please use the `mode` argument instead. + --- failed re-building ‘tilemaps.Rmd’ SUMMARY: processing the following file failed: - ‘simcausal_vignette.Rnw’ + ‘tilemaps.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# skynet - -
- -* Version: 1.4.3 -* GitHub: https://github.com/ropensci/skynet -* Source code: https://github.com/cran/skynet -* Date/Publication: 2022-06-17 13:00:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "skynet")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(skynet) - > - > test_check("skynet") - [ FAIL 1 | WARN 25 | SKIP 4 | PASS 69 ] - - ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ - ... - 14. │ └─base::lapply(args, rlang::eval_tidy, data = data_mask) - 15. │ └─rlang (local) FUN(X[[i]], ...) - 16. └─igraph (local) from(V(x)[y]) - 17. └─lifecycle::deprecate_stop("2.1.0", "from()", ".from()") - 18. └─lifecycle:::deprecate_stop0(msg) - 19. └─rlang::cnd_signal(...) - - [ FAIL 1 | WARN 25 | SKIP 4 | PASS 69 ] - Error: Test failures - Execution halted - ``` - ## In both * checking dependencies in R code ... NOTE ``` - Namespace in Imports field not imported from: ‘maps’ + Namespace in Imports field not imported from: ‘lwgeom’ All declared Imports should be used. ```