* using log directory ‘/srv/hornik/tmp/CRAN/Platypus.Rcheck’
* using R Under development (unstable) (2024-02-11 r85891)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘Platypus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Platypus’ version ‘3.5.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Alexander Yermanos <ayermanos@gmail.com>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  immunogenomics (4:512)
  scSeq (4:174)
  transcriptional (4:318)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2023-06-15 as issues were not corrected
    in time.

Found the following (possibly) invalid URLs:
  URL: https://github.com/alexyermanos/Platypus/blob/Functions/R/VDJ_GEX_matrix.R
    From: inst/doc/PlatypusV3_agedCNS.html
    Status: 404
    Message: Not Found
  URL: https://github.com/alexyermanos/Platypus/tree/Functions/R
    From: inst/doc/PlatypusV3_agedCNS.html
    Status: 404
    Message: Not Found
  URL: https://www.biorxiv.org/content/10.1101/2022.09.28.509709v1
    From: README.md
    Status: 403
    Message: Forbidden
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Platypus’ can be installed ... [16s/16s] 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [33s/33s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) VDJ_call_MIXCR.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{custom.cmd.call}{This function calls Mixcr via a terminal. The commands are build as follows: FOR DARWIN and LINUX machines: paste0(custom.cmd.call," ", mixcr.directory,"/mixcr.jar ... {mixcr parameters assembled by function}"). FOR WINDOWS machines: paste0(custom.cmd.call," mixcr.jar ... {mixcr parameters assembled by function}") custom.cmd.call defaults to "java -jar". In case different MIXCR installations, changing this to meet your systems requirements may be necessary.}
       |                                                                                                                                                                                                ^
checkRd: (-1) VDJ_call_MIXCR.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{custom.cmd.call}{This function calls Mixcr via a terminal. The commands are build as follows: FOR DARWIN and LINUX machines: paste0(custom.cmd.call," ", mixcr.directory,"/mixcr.jar ... {mixcr parameters assembled by function}"). FOR WINDOWS machines: paste0(custom.cmd.call," mixcr.jar ... {mixcr parameters assembled by function}") custom.cmd.call defaults to "java -jar". In case different MIXCR installations, changing this to meet your systems requirements may be necessary.}
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) VDJ_call_RECON.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{recon.directory}{directory containing recon executable. Defaults to {working directory}/Recon}
       |                                                                           ^
* 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 ... [3s/3s] 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 ... [28s/28s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [5s/5s] 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