* using log directory 'd:/RCompile/CRANincoming/R-devel/MiscMetabar.Rcheck'
* using R Under development (unstable) (2025-03-09 r87914 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 'MiscMetabar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MiscMetabar' version '0.14.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [56s] NOTE
Maintainer: 'Adrien Taudière <adrien.taudiere@zaclys.net>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Metabarcoding (3:36)
  bioinformatics (7:250)
  metabarcoding (7:94)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2025-02-20 for policy violation.

  On Internet access. Even after update.

Found the following (possibly) invalid URLs:
  URL: https://www.gnu.org/licenses/gpl-3.0
    From: README.md
    Status: Error
    Message: Timeout was reached [www.gnu.org]: Failed to connect to www.gnu.org port 443 after 21144 ms: Could not connect to server
* 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 whether package 'MiscMetabar' 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 ... [13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s] OK
* checking whether the package can be unloaded cleanly ... [12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s] OK
* checking loading without being on the library search path ... [13s] 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 ... [79s] 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 ... OK
* 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 ... [60s] ERROR
Running examples in 'MiscMetabar-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter_trim
> ### Title: A wrapper of the function 'dada2::filterAndTrim()' to use in
> ###   targets pipeline
> ### Aliases: filter_trim
> 
> ### ** Examples
> 
> testFastqs_fw <- c(
+   system.file("extdata", "sam1F.fastq.gz", package = "dada2"),
+   system.file("extdata", "sam2F.fastq.gz", package = "dada2")
+ )
> testFastqs_rev <- c(
+   system.file("extdata", "sam1R.fastq.gz", package = "dada2"),
+   system.file("extdata", "sam2R.fastq.gz", package = "dada2")
+ )
> 
> filt_fastq_fw <- filter_trim(testFastqs_fw, output_fw = tempdir())
> derep_fw <- derepFastq(filt_fastq_fw[1])
> derep_fw
$sam1F.fastq.gz
derep-class: R object describing dereplicated sequencing reads
$uniques: 1500 reads in 896 unique sequences
  Sequence lengths: min=250, median=250, max=250
$quals: Quality matrix dimension:  896 250
  Consensus quality scores: min=7, median=36, max=38
$map: Map from reads to unique sequences:  4 155 627 265 5 ...

$sam2F.fastq.gz
derep-class: R object describing dereplicated sequencing reads
$uniques: 1500 reads in 909 unique sequences
  Sequence lengths: min=250, median=250, max=250
$quals: Quality matrix dimension:  909 250
  Consensus quality scores: min=7, median=36, max=38
$map: Map from reads to unique sequences:  890 14 2 246 797 ...

> 
> filt_fastq_pe <- filter_trim(testFastqs_fw,
+   testFastqs_rev,
+   output_fw = tempdir("fw"),
+   output_rev = tempdir("rev")
+ )
Error in tempdir(check) : NA in coercion to boolean
Calls: filter_trim -> <Anonymous> -> tempdir
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [57s] ERROR
  Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MiscMetabar)
  Loading required package: phyloseq
  Loading required package: ggplot2
  Loading required package: dada2
  Loading required package: Rcpp
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: purrr
  
  Attaching package: 'purrr'
  
  The following object is masked from 'package:testthat':
  
      is_null
  
  > 
  > test_check("MiscMetabar")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 75 | PASS 78 ]
  
  ══ Skipped tests (75) ══════════════════════════════════════════════════════════
  • On CRAN (63): 'test_adonis.R:1:1', 'test_controls.R:7:3',
    'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
    'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
    'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
    'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
    'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
    'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',
    'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
    'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',
    'test_figures_biplot.R:52:3', 'test_figures_misc.R:26:3',
    'test_figures_misc.R:35:3', 'test_figures_beta_div.R:22:3',
    'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
    'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
    'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
    'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
    'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
    'test_figures_beta_div.R:387:3', 'test_figures_summary_plot.R:9:3',
    'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',
    'test_krona.R:7:3', 'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
    'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
    'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
    'test_figures_taxo.R:379:3', 'test_phyloseq_class.R:10:3',
    'test_phyloseq_class.R:51:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
    'test_subset.R:7:3', 'test_subset.R:18:3', 'test_table_functions.R:34:5',
    'test_table_functions.R:47:5', 'test_targets.R:5:3', 'test_targets.R:56:3',
    'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
    'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
    'test_misc.R:30:3', 'test_misc.R:97:3'
  • On Windows (12): 'test_figures_misc.R:10:3', 'test_figures_misc.R:18:3',
    'test_figures_beta_div.R:208:3', 'test_figures_beta_div.R:401:3',
    'test_figures_beta_div.R:413:3', 'test_figures_taxo.R:413:3',
    'test_phyloseq_class.R:92:3', 'test_rw.R:38:3', 'test_table_functions.R:5:3',
    'test_table_functions.R:18:3', 'test_targets.R:83:3', 'test_targets.R:128:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_targets.R:181:3'): sample_data_with_new_names function works fine ──
  Error in `tempdir(check)`: NA in coercion to boolean
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test_targets.R:181:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─MiscMetabar::filter_trim(...)
   10. │ └─dada2::filterAndTrim(...)
   11. └─base::tempdir("fw")
  
  [ FAIL 1 | WARN 0 | SKIP 75 | PASS 78 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s] OK
* checking PDF version of manual ... [37s] OK
* checking HTML version of manual ... [28s] OK
* DONE
Status: 2 ERRORs, 1 NOTE