* using log directory ‘/srv/hornik/tmp/CRAN/debar.Rcheck’
* using R Under development (unstable) (2024-01-08 r85794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (3)
    Debian flang-new version 17.0.6 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘debar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debar’ version ‘0.1.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Cameron M. Nugent <camnugent@gmail.com>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Barcode (3:46)
  COI (3:39, 8:79, 14:27)
  Denoiser (3:26)
  Durbin (11:73)
  PHMM (11:12, 13:72)
  Viterbi (11:28)
  al (11:83)
  barcode (8:40, 14:31)
  cytochrome (8:55)
  denoising (7:71)
  et (11:80)
  indel (15:53)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-08-19 as email to the maintainer is
    undeliverable.

Found the following (possibly) invalid URLs:
  URL: https://codecov.io/gh/CNuge/debar (moved to https://app.codecov.io/gh/CNuge/debar)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://support.rstudio.com/hc/en-us/articles/200711843-Working-Directories-and-Workspaces (moved to https://support.posit.co/hc/en-us/articles/200711843-Working-Directories-and-Workspaces)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://travis-ci.com/CNuge/debar (moved to https://www.travis-ci.com/CNuge/debar)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://www.pacb.com/products-and-services/sequel-system/ (moved to https://www.pacb.com/technology/hifi-sequencing/sequel-system/)
    From: README.md
    Status: 301
    Message: Moved Permanently
  For content that is 'Moved Permanently', please change http to https,
  add trailing slashes, or replace the old by the new URL.

The Title field should be in title case. Current version is:
‘A Post-Clustering Denoiser for COI-5P Barcode Data’
In title case that is:
‘A Post-Clustering Denoiser for COI-5p Barcode Data’
* checking package namespace information ... OK
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* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘debar’ can be installed ... [1s/1s] 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) aa_check.Rd:26: Lost braces
    26 | a class object of code{"ccs_reads"}
       |                       ^
checkRd: (-1) adjust.Rd:23: Lost braces
    23 | a class object of code{"ccs_reads"}
       |                       ^
checkRd: (-1) denoise.Rd:87: Lost braces
    87 | a class object of code{"DNAseq"}
       |                       ^
checkRd: (-1) frame.Rd:37: Lost braces
    37 | a class object of code{"DNAseq"}
       |                       ^
checkRd: (-1) outseq.Rd:29: Lost braces
    29 | a class object of code{"ccs_reads"}
       |                       ^
checkRd: (-1) write_fasta.Rd:24: Lost braces
    24 | a class object of code{"DNAseq"}
       |                       ^
checkRd: (-1) write_fastq.Rd:28: Lost braces
    28 | a class object of code{"DNAseq"}
       |                       ^
checkRd: (-1) write_wrapper.Rd:31: Lost braces
    31 | a class object of code{"DNAseq"}
       |                       ^
* checking Rd metadata ... OK
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* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [30s/30s] OK
  Running ‘testthat.R’ [29s/29s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [6s/6s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs