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chore: Update revdepcheck results
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krlmlr committed Jan 11, 2024
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9 changes: 3 additions & 6 deletions revdep/README.md
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# 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__ | | |
|[pcalg](problems.md#pcalg)|2.7-9 |__+1__ | |3 |
|[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__ | | |

15 changes: 2 additions & 13 deletions revdep/cran.md
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## 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.

### New problems
(This reports the first line of each new failure)

* bnstruct
checking tests ... ERROR

* countland
checking tests ... ERROR

Expand Down Expand Up @@ -46,9 +43,6 @@ Issues with CRAN packages are summarised below.
* molnet
checking examples ... ERROR

* NAIR
checking tests ... ERROR

* nat
checking tests ... ERROR

Expand Down Expand Up @@ -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
Expand Down
228 changes: 7 additions & 221 deletions revdep/problems.md
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# bnstruct

<details>

* 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

</details>

## 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 <RETURN> 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

<details>
Expand Down Expand Up @@ -355,10 +287,10 @@ Run `revdepcheck::cloud_details(, "ggnetwork")` for more info
<details>
* 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
Expand All @@ -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
Expand Down Expand Up @@ -567,56 +499,6 @@ Run `revdepcheck::cloud_details(, "molnet")` for more info
Execution halted
```
# NAIR
<details>
* 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
</details>
## 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
<details>
Expand Down Expand Up @@ -662,10 +544,10 @@ Run `revdepcheck::cloud_details(, "nat")` for more info
<details>
* 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
Expand Down Expand Up @@ -1084,102 +966,6 @@ Run `revdepcheck::cloud_details(, "riverconn")` for more info
Execution halted
```
# signnet
<details>
* 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
</details>
## 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 -> <Anonymous> -> 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
<details>
Expand Down

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