Fix failing tests

[talgalili]

Log from winbuild

* using log directory 'd:/RCompile/CRANguest/R-devel/dendextend.Rcheck'
* using R Under development (unstable) (2024-11-11 r87319 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'dendextend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dendextend' version '1.19.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [51s] OK
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'dendextend' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [26s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'all.equal.dendrogram.Rd':
all.equal.dendlist
  Code: function(target, current, ...)
  Docs: function(target, current, use.edge.length = TRUE,
                 use.tip.label.order = FALSE, use.tip.label = TRUE,
                 use.topology = TRUE, tolerance =
                 .Machine$double.eps^0.5, scale = NULL, ...)
  Argument names in docs not in code:
    use.edge.length use.tip.label.order use.tip.label use.topology
    tolerance scale
  Mismatches in argument names:
    Position: 3 Code: ... Docs: use.edge.length

* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [17s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [117s] ERROR
  Running 'testthat.R' [117s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.19.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  You may ask questions at stackoverflow, use the r and dendextend tags: 
  	 https://stackoverflow.com/questions/tagged/dendextend
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  ch. 1 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; ch. 2 @ h= 2 ; ch. 1 @ h= 0 ; ch. 2 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; ch. 1 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; ch. 2 @ h= 2 ; ch. 1 @ h= 0 ; ch. 2 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; Tracing dendrogram_data(dend) step 6 
  ch. 1 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; ch. 2 @ h= 2 ; ch. 1 @ h= 0 ; ch. 2 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; Tracing dendrogram_data(dend) step 15 
  ch. 1 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; ch. 2 @ h= 2 ; ch. 1 @ h= 0 ; ch. 2 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; Tracing dendrogram_data(dend) step 15 
  ch. 1 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; ch. 2 @ h= 2 ; ch. 1 @ h= 0 ; ch. 2 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; Tracing dendrogram_data(dend) step 15 
  ch. 1 @ h= 1 ; ch. 1 @ h= ; ch. 2 @ h= 0 ; ch. 2 @ h= 2 ; ch. 1 @ h= 0 ; ch. 2 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; Tracing dendrogram_data(dend) step 15 
  ch. 1 @ h= 1 ; ch. 1 @ h= ; ch. 2 @ h= 0 ; ch. 2 @ h= 2 ; ch. 1 @ h= 0 ; ch. 2 @ h= 1 ; ch. 1 @ h= 0 ; ch. 2 @ h= 0 ; [ FAIL 4 | WARN 1 | SKIP 0 | PASS 800 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-color_branches.R:33:4'): color_branches works ────────────────
  color_branches(hc) not equal to color_branches(dend).
  Attributes: < Names: 3 string mismatches >
  Attributes: < Length mismatch: comparison on first 4 components >
  Attributes: < Component 2: Modes: list, numeric >
  Attributes: < Component 2: names for target but not for current >
  Attributes: < Component 2: Component 1: Modes: character, numeric >
  Attributes: < Component 2: Component 1: target is character, current is numeric >
  Attributes: < Component 3: Mean relative difference: 0.25 >
  Attributes: < Component 4: Mean relative difference: 0.675 >
  Component 1: Attributes: < Names: 3 string mismatches >
  ...
  ── Failure ('test-color_branches.R:50:4'): color_branches works ────────────────
  `result1` not equal to `result2`.
  Component 1: Attributes: < Names: 3 string mismatches >
  Component 1: Attributes: < Length mismatch: comparison on first 4 components >
  Component 1: Attributes: < Component "edgePar": Length mismatch: comparison on first 1 components >
  Component 1: Attributes: < Component 3: Mean relative difference: 1 >
  Component 1: Attributes: < Component 4: Mean relative difference: 0.75 >
  Component 2: Attributes: < Names: 3 string mismatches >
  Component 2: Attributes: < Length mismatch: comparison on first 4 components >
  Component 2: Attributes: < Component "edgePar": Length mismatch: comparison on first 1 components >
  Component 2: Attributes: < Component 3: Mean relative difference: 0.5 >
  ...
  ── Failure ('test-prune.R:38:4'): prune works for non-dendrogram objects ───────
  as.dendrogram(result) not equal to prune_leaf(dend, "Florida").
  Component 2: Component 2: Component 1: Component 2: Component 2: Mean relative difference: 0.111
  ── Failure ('test-prune.R:43:4'): prune works for non-dendrogram objects ───────
  as.dendrogram(result) not equal to prune_leaf(dend, "Florida").
  Component 2: Component 2: Component 1: Component 2: Component 2: Mean relative difference: 0.111
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 800 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [151s] OK
* checking PDF version of manual ... [29s] OK
* checking HTML version of manual ... [24s] OK
* DONE
Status: 1 ERROR, 1 WARNING

[talgalili]

Hi @alecbuetow
I ran the most recent version in winbuild and found the above errors, could you please take a look?

[alecbuetow]

On it

[alecbuetow]

It looks like the windows version doesn't like expect_equal(dend1, dend2) even if the dendrograms are the same. I changed the tests to account for this

[talgalili]

Thanks @alecbuetow
I'm taking a look.

Ref: ed39cec

[talgalili]

Thanks for the work @alecbuetow
I checked the latest version and it's now does not raise any errors or warnings.

And also I see we're at 98% - amazing!

Horray :)

[talgalili]

@alecbuetow in terms of next steps, some questions:

1. Do you intend to work some more on the test coverage? (we're at 98%, are you going to try to reach 100%, of stop around here?)
2. Are you interested in more tasks for me to tag you on?

[alecbuetow]

I'm shooting for 100%! I'd love to keep working on tasks; I'm gonna stick to dendextend for now since I'll be fairly busy for the next few months. Happy to get acquainted with other packages in the future

[talgalili]

@alecbuetow sounds amazing!

Some tasks I'd love for you to take a look:

1. Rotate labels for ggplot dendrogram, this can help with creating circular dendrograms using ggdend: Rotate labels for ggplot dendrogram #44
2. related: circlize_dendrogram can benefit from some work, see:
   Distance between leaf and label in circlize_dendrogram() #116
3. Feel free to go over other open tasks and discuss if the issue is already resolved, or if it should be resolved: https://github.com/talgalili/dendextend/issues
4. In the future, feel free to also contribute to heatmaply (which relies on dendextend): https://github.com/talgalili/heatmaply/issues

[alecbuetow]

Excellent, will do!