From 5a437fe761a1b33cfb5c3026cc060580ca22f02a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Fri, 12 Jan 2024 00:48:53 +0100 Subject: [PATCH] chore: Update revdepcheck results --- revdep/README.md | 9 +- revdep/cran.md | 15 +-- revdep/problems.md | 228 ++------------------------------------------- 3 files changed, 12 insertions(+), 240 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 187faa054e..b5e0b0847b 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,24 +1,22 @@ # Revdeps -## New problems (25) +## New problems (22) |package |version |error |warning |note | |:-----------------|:-------|:------|:-------|:----| -|[bnstruct](problems.md#bnstruct)|1.0.14 |__+1__ |1 | | |[countland](problems.md#countland)|0.1.1 |__+1__ | | | |[DiagrammeR](problems.md#diagrammer)|1.0.10 |__+1__ | |1 | |[dnet](problems.md#dnet)|1.1.7 |__+1__ | | | |[dragon](problems.md#dragon)|1.2.1 |__+1__ | |2 | |[EGAnet](problems.md#eganet)|2.0.3 |__+1__ | |1 | |[ggnetwork](problems.md#ggnetwork)|0.5.12 |__+1__ | |1 | -|[inferCSN](problems.md#infercsn)|0.99.8 |__+1__ | |1 | +|[inferCSN](problems.md#infercsn)|0.99.9 |__+1__ | |1 | |[intergraph](problems.md#intergraph)|2.0-3 |__+1__ | | | |[manynet](problems.md#manynet)|0.3.0 |__+1__ | |2 | |[migraph](problems.md#migraph)|1.2.1 |__+1__ | | | |[molnet](problems.md#molnet)|0.1.0 |__+1__ | | | -|[NAIR](problems.md#nair)|1.0.2 |__+1__ | |1 | |[nat](problems.md#nat)|1.8.23 |__+1__ | | | -|[nbTransmission](problems.md#nbtransmission)|1.1.2 |__+2__ | | | +|[nbTransmission](problems.md#nbtransmission)|1.1.3 |__+2__ | | | |[netcom](problems.md#netcom)|2.1.6 |__+2__ | |1 | |[nosoi](problems.md#nosoi)|1.1.0 |__+1__ | | | |[oddnet](problems.md#oddnet)|0.1.0 |__+1__ | | | @@ -26,7 +24,6 @@ |[phyloseqGraphTest](problems.md#phyloseqgraphtest)|0.1.0 |__+2__ | |2 | |[rgraph6](problems.md#rgraph6)|2.0-3 |__+1__ | | | |[riverconn](problems.md#riverconn)|0.3.28 |__+1__ | | | -|[signnet](problems.md#signnet)|1.0.3 |__+3__ | |1 | |[tidygraph](problems.md#tidygraph)|1.3.0 |__+2__ | | | |[VertexSort](problems.md#vertexsort)|0.1-1 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index fcacc93acc..799a678e95 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,8 +1,8 @@ ## revdepcheck results -We checked 26 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 23 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 25 new problems + * We saw 22 new problems * We failed to check 0 packages Issues with CRAN packages are summarised below. @@ -10,9 +10,6 @@ Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* bnstruct - checking tests ... ERROR - * countland checking tests ... ERROR @@ -46,9 +43,6 @@ Issues with CRAN packages are summarised below. * molnet checking examples ... ERROR -* NAIR - checking tests ... ERROR - * nat checking tests ... ERROR @@ -79,11 +73,6 @@ Issues with CRAN packages are summarised below. * riverconn checking re-building of vignette outputs ... ERROR -* signnet - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... ERROR - * tidygraph checking examples ... ERROR checking tests ... ERROR diff --git a/revdep/problems.md b/revdep/problems.md index 87820f6567..4c536ebac1 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,71 +1,3 @@ -# bnstruct - -
- -* Version: 1.0.14 -* GitHub: NA -* Source code: https://github.com/cran/bnstruct -* Date/Publication: 2022-11-30 14:10:02 UTC -* Number of recursive dependencies: 104 - -Run `revdepcheck::cloud_details(, "bnstruct")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > test_check("bnstruct") - Loading required package: bnstruct - Loading required package: bitops - Loading required package: igraph - - Attaching package: 'igraph' - ... - ▆ - 1. └─bnstruct::InferenceEngine(network) at test_em.R:6:1 - 2. ├─bnstruct::build.junction.tree(object, dag) - 3. └─bnstruct::build.junction.tree(object, dag) - 4. └─bnstruct:::clique.tree(graph) - 5. └─igraph::cliques(ig, min = NULL, max = NULL) - - [ FAIL 1 | WARN 2 | SKIP 1 | PASS 1 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘bnstruct.Rnw’ using Sweave - Error: processing vignette 'bnstruct.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'bnstruct.tex' failed. - LaTeX errors: - ! LaTeX Error: File `pdfpages.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.6 ^^M - - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘bnstruct.Rnw’ - - SUMMARY: processing the following file failed: - ‘bnstruct.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - # countland
@@ -355,10 +287,10 @@ Run `revdepcheck::cloud_details(, "ggnetwork")` for more info
-* Version: 0.99.8 +* Version: 0.99.9 * GitHub: https://github.com/mengxu98/inferCSN * Source code: https://github.com/cran/inferCSN -* Date/Publication: 2023-12-04 05:00:02 UTC +* Date/Publication: 2024-01-10 05:53:10 UTC * Number of recursive dependencies: 100 Run `revdepcheck::cloud_details(, "inferCSN")` for more info @@ -379,9 +311,9 @@ Run `revdepcheck::cloud_details(, "inferCSN")` for more info > ### ** Examples > > library(inferCSN) - > data("exampleMatrix") - > weightDT <- inferCSN(exampleMatrix) - > g <- dynamic.networks(weightDT, regulators = weightDT[1, 1]) + > data("example_matrix") + > weight_table <- inferCSN(example_matrix) + > g <- dynamic.networks(weight_table, regulators = weight_table[1, 1]) Error in fortify.igraph(x, ...) : layout matrix dimensions do not match network size Calls: dynamic.networks -> ggnetwork -> fortify.igraph @@ -567,56 +499,6 @@ Run `revdepcheck::cloud_details(, "molnet")` for more info Execution halted ``` -# NAIR - -
- -* Version: 1.0.2 -* GitHub: https://github.com/mlizhangx/Network-Analysis-for-Repertoire-Sequencing- -* Source code: https://github.com/cran/NAIR -* Date/Publication: 2023-09-27 10:20:08 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "NAIR")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(NAIR) - Welcome to NAIR: Network Analysis of Immune Repertoire. - Get started using `vignette("NAIR")`, or by visiting - https://mlizhangx.github.io/Network-Analysis-for-Repertoire-Sequencing-/ - > - > test_check("NAIR") - ... - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test_functions.R:722:3'): addClusterMembership works ────────────── - net$details$clusters_in_network (`actual`) not equal to c(fast_greedy = 20, leiden = 55) (`expected`). - - `actual`: 20 53 - `expected`: 20 55 - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1219 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.1Mb - sub-directories of 1Mb or more: - libs 6.6Mb - ``` - # nat
@@ -662,10 +544,10 @@ Run `revdepcheck::cloud_details(, "nat")` for more info
-* Version: 1.1.2 +* Version: 1.1.3 * GitHub: https://github.com/sarahleavitt/nbTransmission * Source code: https://github.com/cran/nbTransmission -* Date/Publication: 2021-01-06 19:50:03 UTC +* Date/Publication: 2024-01-10 19:53:14 UTC * Number of recursive dependencies: 124 Run `revdepcheck::cloud_details(, "nbTransmission")` for more info @@ -1084,102 +966,6 @@ Run `revdepcheck::cloud_details(, "riverconn")` for more info Execution halted ``` -# signnet - -
- -* Version: 1.0.3 -* GitHub: https://github.com/schochastics/signnet -* Source code: https://github.com/cran/signnet -* Date/Publication: 2023-12-15 20:30:02 UTC -* Number of recursive dependencies: 105 - -Run `revdepcheck::cloud_details(, "signnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘signnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: complex_walks - > ### Title: Count Walks in complex signed network - > ### Aliases: complex_walks - > - > ### ** Examples - > - > g <- sample_islands_signed(2, 10, 1, 10) - > g <- as_complex_edges(g, attr = "type") - > complex_walks(g, attr = "type", k = 3) - Error in get.adjacency.dense(graph, type = type, attr = attr, weights = NULL, : - Matrices must be either numeric or logical, and the edge attribute is not - Calls: complex_walks ... as_adj_complex -> -> get.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(signnet) - > - > test_check("signnet") - [ FAIL 5 | WARN 13 | SKIP 0 | PASS 88 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - Backtrace: - ▆ - 1. └─signnet::complex_walks(g, "type", 3) at test-complex_matrices.R:171:3 - 2. └─signnet::as_adj_complex(g, attr) - 3. └─igraph::as_adj(g, type = "both", attr, sparse = FALSE) - 4. └─igraph:::get.adjacency.dense(...) - - [ FAIL 5 | WARN 13 | SKIP 0 | PASS 88 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘blockmodeling.Rmd’ using rmarkdown - --- finished re-building ‘blockmodeling.Rmd’ - - --- re-building ‘centrality.Rmd’ using rmarkdown - --- finished re-building ‘centrality.Rmd’ - - --- re-building ‘complex_matrices.Rmd’ using rmarkdown - - Quitting from lines 54-55 [pna_adj] (complex_matrices.Rmd) - ... - --- finished re-building ‘signed_networks.Rmd’ - - --- re-building ‘structural_balance.Rmd’ using rmarkdown - --- finished re-building ‘structural_balance.Rmd’ - - SUMMARY: processing the following file failed: - ‘complex_matrices.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 11.0Mb - sub-directories of 1Mb or more: - data 1.0Mb - libs 8.9Mb - ``` - # tidygraph