##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqArchR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqArchR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/seqArchR.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqArchR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqArchR’ version ‘1.11.0’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘seqArchR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘seqArchR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seqArchR
> ### Title: seqArchR: A package for de novo discovery of different sequence
> ###   architectures
> ### Aliases: seqArchR
> 
> ### ** Examples
> 
> 
> 
> # Here,we re-use the example input sequences and one-hot encoded matrix
> # shipped with seqArchR. Please see examples in the corresponding man pages
> # for generating a one-hot encoded input matrix from raw FASTA sequences
> # in `prepare_data_from_FASTA`
> #
> inputSeqsMat <- readRDS(system.file("extdata", "tssSinuc.rds",
+                              package = "seqArchR", mustWork = TRUE))
> 
> inputSeqsRaw <- readRDS(system.file("extdata", "tssSeqsRaw.rds",
+                              package = "seqArchR", mustWork = TRUE))
> 
> # Set seqArchR configuration
> seqArchRconfig <- seqArchR::set_config(
+     parallelize = TRUE,
+     n_cores = 2,
+     n_runs = 100,
+     k_min = 1,
+     k_max = 20,
+     mod_sel_type = "stability",
+     bound = 10^-8,
+     chunk_size = 100,
+     flags = list(debug = FALSE, time = TRUE, verbose = TRUE,
+         plot = FALSE)
+ )
> 
> # Run seqArchR
> seqArchRresult <- seqArchR::seqArchR(config = seqArchRconfig,
+                           seqs_ohe_mat = inputSeqsMat,
+                           seqs_raw = inputSeqsRaw,
+                           seqs_pos = seq(1,100,by=1),
+                           total_itr = 2,
+                           set_ocollation = c(TRUE, FALSE))
── Setting up ──────────────────────────────────────────────────────────────────
ℹ Parallelization: Yes
ℹ Model selection by factor stability
ℹ Bound: 1e-08

── Iteration 1 of 2 [1 chunk] ──────────────────────────────────────────────────

── Outer chunk 1 of 1 [Size: 200] ──

── Inner chunk 1 of 2 [Size: 100] 
Error: BiocParallel errors
  2 remote errors, element index: 1, 51
  98 unevaluated and other errors
  first remote error:
Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn'
Run `reticulate::py_last_error()` for details.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:186:5
    2.   └─seqArchR:::process_innerChunk(...)
    3.     └─base::lapply(...)
    4.       └─seqArchR (local) FUN(X[[i]], ...)
    5.         └─seqArchR:::.handle_chunk_w_NMF2(...)
    6.           └─seqArchR:::.stability_model_select_pyNMF2(...)
    7.             └─seqArchR:::.perform_multiple_NMF_runs(...)
    8.               ├─BiocParallel::bplapply(...)
    9.               └─BiocParallel::bplapply(...)
   10.                 └─BiocParallel:::.bpinit(...)
  
  [ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/seqArchR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqArchR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘seqArchR’ ...
** this is package ‘seqArchR’ version ‘1.11.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (seqArchR)

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(seqArchR)
> 
> test_check("seqArchR")
[[1]]

NULL
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test_plot_arch_for_clusters.R:31:5',
  'test_plot_ggseqlogo.R:75:3', 'test_plot_heatmap.R:61:3',
  'test_seqs_image_representation.R:15:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_seqArchR_main.R:48:5'): seqArchR (stability) works when timeFlag is FALSE/checkpointing ──
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  49 unevaluated and other errors
  first remote error:
Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn'
Run `reticulate::py_last_error()` for details.

Backtrace:
     ▆
  1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:48:5
  2.   └─seqArchR:::process_innerChunk(...)
  3.     └─base::lapply(...)
  4.       └─seqArchR (local) FUN(X[[i]], ...)
  5.         └─seqArchR:::.handle_chunk_w_NMF2(...)
  6.           └─seqArchR:::.stability_model_select_pyNMF2(...)
  7.             └─seqArchR:::.perform_multiple_NMF_runs(...)
  8.               ├─BiocParallel::bplapply(...)
  9.               └─BiocParallel::bplapply(...)
 10.                 └─BiocParallel:::.bpinit(...)
── Error ('test_seqArchR_main.R:149:5'): seqArchR (cv) works when timeFlag is FALSE ──
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  2 remote errors, element index: 1, 26
  48 unevaluated and other errors
  first remote error:
Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn'
Run `reticulate::py_last_error()` for details.

Backtrace:
     ▆
  1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:149:5
  2.   └─seqArchR:::process_innerChunk(...)
  3.     └─base::lapply(...)
  4.       └─seqArchR (local) FUN(X[[i]], ...)
  5.         └─seqArchR:::.handle_chunk_w_NMF2(...)
  6.           └─seqArchR:::.cv_model_select_pyNMF2(...)
  7.             └─seqArchR:::performSearchForK(...)
  8.               ├─base::unlist(...)
  9.               ├─BiocParallel::bplapply(...)
 10.               └─BiocParallel::bplapply(...)
 11.                 └─BiocParallel:::.bpinit(...)
── Error ('test_seqArchR_main.R:186:5'): seqArchR (stability) works when debug & timeFlag is FALSE ──
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  49 unevaluated and other errors
  first remote error:
Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn'
Run `reticulate::py_last_error()` for details.

Backtrace:
     ▆
  1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:186:5
  2.   └─seqArchR:::process_innerChunk(...)
  3.     └─base::lapply(...)
  4.       └─seqArchR (local) FUN(X[[i]], ...)
  5.         └─seqArchR:::.handle_chunk_w_NMF2(...)
  6.           └─seqArchR:::.stability_model_select_pyNMF2(...)
  7.             └─seqArchR:::.perform_multiple_NMF_runs(...)
  8.               ├─BiocParallel::bplapply(...)
  9.               └─BiocParallel::bplapply(...)
 10.                 └─BiocParallel:::.bpinit(...)

[ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ]
Error: Test failures
Execution halted