new tests by Gian77 · Pull Request #30 · germs-lab/BRCore

Gian77 · 2025-05-23T00:36:18Z

I added the two checks for the multi_rarefy() and the do_phyloseq(). I tested thm locally and they seem to work. I used the test_phyloseq dataset for the test because the esophagous is really too small.

jibarozzo · 2025-05-23T01:55:18Z

Checks are not passing. This branch seems to be out of date compared to develop.

…q.Rd

modified: NAMESPACE modified: tests/testthat/test-multi_rarefy.R

modified: tests/testthat/test-do_phyloseq.R

jibarozzo · 2025-05-28T20:28:39Z

rarefied_physeq <- do_phyloseq(physeq = GlobalPatterns, otu_rare=rarefied_data )
head(otu_table(rarefied_physeq))
Error in otu_table(rarefied_physeq) : could not find function "otu_table"
Calls: head
Execution halted

Gian77 · 2025-05-28T20:41:50Z

What should I do here next @jibarozzo @B-Kristy ?

jibarozzo · 2025-05-28T20:49:43Z

The errors in the check point to: https://github.com/germs-lab/BRCore/actions/runs/15202638884/job/42759431560?pr=30

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 52 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-do_phyloseq.R:15:5'): phyloseq object correctly created ──────
all(read_counts == read_counts[1]) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-multi_rarefy.R:12:5'): rarefaction worked correctly ──────────
all(rowSums(otu_table_rare) == rowSums(otu_table_rare)[1]) is not TRUE

`actual`:   FALSE
`expected`: TRUE

I am currently working on another where I think I inherited these error. Let's see what the tests say.

jibarozzo · 2025-05-28T20:55:40Z

@Gian77

This is what you need to do. In your do_phyloseq.R update this:

Option 1

#' @examples
#' \dontrun{
#' # Load example data
#' data(GlobalPatterns, package = "phyloseq")
#'
	@@ -23,6 +24,7 @@
#' 
#' rarefied_physeq <- do_phyloseq(physeq = GlobalPatterns, otu_rare=rarefied_data )
#' head(otu_table(rarefied_physeq))
#' }

Note that I am calling \dontrun{} on the example this prevents the example from running.

**Option 2**
#' @examples
#' library(phyloseq)
#' # Load example data
#' data(GlobalPatterns, package = "phyloseq")
#'
	@@ -23,6 +24,7 @@
#' 
#' rarefied_physeq <- do_phyloseq(physeq = GlobalPatterns, otu_rare=rarefied_data )
#' head(otu_table(rarefied_physeq))
#'

You load phyloseq package so the example runs.

Then uodate the man pages, NAMESPACE, etc...

Gian77 · 2025-05-29T14:22:21Z

@jibarozzo now the error is different is at line 252

  > rarefied_physeq <- do_phyloseq(physeq = GlobalPatterns, otu_rare=rarefied_data )
  Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'samples' in selecting a method for function 'prune_samples': error in evaluating the argument 'object' in selecting a method for function 'otu_table': error in evaluating the argument 'taxa' in selecting a method for function 'prune_taxa': error in evaluating the argument 'object' in selecting a method for function 'otu_table': invalid class “otu_table” object: 
   OTU abundance data must have non-zero dimensions.
  Calls: do_phyloseq ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
  Execution halted

it seems the rarefied_data is empty or something...

and at 227 there is this

❯ checking examples ... [53s/55s] ERROR
  Running examples in ‘BRCore-Ex.R’ failed
  The error most likely occurred in:

what is BRCore-Ex.R?

jibarozzo · 2025-05-29T16:14:08Z

BRCore-Ex.R a script that gets created when it runs the tests.

Gian77 · 2025-05-29T16:41:52Z

BRCore-Ex.R a script that gets created when it runs the tests.

ok, then I will just add the \dontrun{} and see if it goes through.

Gian77 · 2025-06-13T00:30:46Z

develop is much ahead than checks... Will try to resolve this and try again... ;)

jibarozzo · 2025-06-13T20:40:37Z

 import(rlang)
 import(tibble)
 import(tidyr)
+import(tidyverse)


@Gian77 Let's not import "tidyverse" completely. See https://stackoverflow.com/questions/44992890/including-tidyverse-packages-in-another-package

The tests are failing because you updated NAMESPACE but not DESCRIPTION. First update DESCRIPTION then NAMESPACE. Everything declared in the description must be declared in namespece, and vice versa.

jibarozzo · 2025-06-13T20:43:47Z

Where are you importing "furrr" and tidyverse"?

jibarozzo · 2025-06-13T20:49:25Z

 export(is_hpc_environment)
 export(multi_rarefy)
 export(nmds_screen_parallel)
+export(parallel_multi_rarefy)


Where is this function?

…ts/Depends entries: 'furrr', 'tidyverse'" introduced by undeclared exports and mismatch between NAMESPACE and DESCRIPTION.

jibarozzo · 2025-06-13T20:58:15Z

Submitted the requested changes. Let's see if tests pass. If they do, I'll merge tomorrow.

jibarozzo · 2025-06-13T21:05:34Z

@Gian77 Once I solved the NAMESPACE and DESCRIPTION issues we encounter a new error. This time in the tests themselves.

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-do_phyloseq.R:15:5'): phyloseq object correctly created ──────
all(read_counts == read_counts[1]) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-multi_rarefy.R:12:5'): rarefaction worked correctly ──────────
all(rowSums(otu_table_rare) == rowSums(otu_table_rare)[1]) is not TRUE

`actual`:   FALSE
`expected`: TRUE

jibarozzo · 2025-06-13T21:13:32Z

+    read_counts <- sample_sums(test_phyloseq_rare)
+
+    # Test if all the samples have the same number of reads
+    expect_true(all(read_counts == read_counts[1]))


This is the source of error failure in Github actions. In local machine this works. @Gian77

Yeah, locally works... Sorry to have do extra work to fix my push problems :D

Debugging

Gian77 · 2025-07-03T14:51:48Z

Do you think we can reject this PR and close it so we can move forward? I am not sure why does not work...

jibarozzo · 2025-07-08T15:58:32Z

I'm jumping back on this this week. I've been out of office.

jibarozzo · 2025-09-03T16:18:35Z

ok, here we go

Gian77 · 2025-09-03T16:23:58Z

@jibarozzo why is failing on macos?

jibarozzo · 2025-09-03T16:25:24Z

@jibarozzo why is failing on macos?

According to Co-pilot: "The macOS failure likely arises due to implicit differences in R's handling of data structures or file reading between macOS and Ubuntu."

I'll implement some changes in the tests and see. Stay put

Gian77 · 2025-09-03T16:30:06Z

I am more than ready! @jibarozzo

jibarozzo · 2025-09-03T17:28:34Z

@Gian77 checks passed. checks branch pruned. Pull develop for now. I will update main to reflect changes and will let you know.

Gian77 · 2025-09-03T17:29:38Z

@jibarozzo This is great! Thank you. We can keep cranking then now!

new tests

0a76ef0

Gian77 added 6 commits May 22, 2025 22:51

Merge branch 'develop' into checks

8253532

update and check again

ec9bd42

Merge branch 'checks' of github.com:germs-lab/BRCore into checks

c029303

Changes to be committed:modified: NAMESPACE new file: man/do_phylose…

f0888bc

…q.Rd

Changes to be committed:

60c089e

modified: NAMESPACE modified: tests/testthat/test-multi_rarefy.R

Changes to be committed:

a2b1af0

modified: tests/testthat/test-do_phyloseq.R

Gian77 added 3 commits May 28, 2025 21:56

new push with hopefully fixed problems

dd6ba96

test passed for ubunutu not for macos...

fddb218

last try before changing strategy...

5e7371a

Gian77 added 3 commits June 12, 2025 20:09

trying the /dontrun{} option and see if it pass the tests...

0e08c78

trying again...

e564b4b

forgot NAMESPACE...

09df12d

let's see...

56ccca4

jibarozzo requested changes Jun 13, 2025

View reviewed changes

Removing error" Namespace dependencies missing from DESCRIPTION Impor…

5355b56

…ts/Depends entries: 'furrr', 'tidyverse'" introduced by undeclared exports and mismatch between NAMESPACE and DESCRIPTION.

jibarozzo assigned Gian77 and jibarozzo Jun 13, 2025

jibarozzo added the enhancement New feature or request label Jun 13, 2025

jibarozzo added this to the BRCore_v.0.03 release milestone Jun 13, 2025

jibarozzo requested changes Jun 13, 2025

View reviewed changes

jibarozzo and others added 4 commits June 16, 2025 06:54

Adding set_seed argument to ensure reproducibility across OS.

44a1a15

Fix typo

c552ba3

Update test-do_phyloseq.R

1b2fddf

Debugging

Changed test to have hardcoded value.

d297c3a

jibarozzo added 3 commits September 3, 2025 11:51

Hopefully fixing test check fails in GH actions due to OS differences.

de60693

Expecting TRUE is not working.

68459e5

Making sure it counts read depth

1405157

jibarozzo approved these changes Sep 3, 2025

View reviewed changes

jibarozzo merged commit 9f0871b into develop Sep 3, 2025
3 checks passed

jibarozzo deleted the checks branch September 3, 2025 17:26

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