* using log directory 'd:/RCompile/CRANincoming/R-devel/MicroSEC.Rcheck'
* using R Under development (unstable) (2024-07-25 r86925 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MicroSEC/DESCRIPTION' ... OK
* this is package 'MicroSEC' version '2.1.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Masachika Ikegami <ikegamitky@gmail.com>'

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2022-03-31 as check problems were not
    corrected in time.

  Leaves detritus.

The Title field should be in title case. Current version is:
  'Sequence Error Filter for formalin-fixed and paraffin-embedded samples'
In title case that is:
  'Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples'
* 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 'MicroSEC' 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 ... 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 loading without being on the library search path ... 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 ... [19s] 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 ... [303s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                 user system elapsed
fun_homology   189.60   2.41  192.00
fun_read_check 100.64   1.67  102.31
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [283s] ERROR
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown

Quitting from lines 204-205 [unnamed-chunk-2] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'my-vignette.Rmd'

SUMMARY: processing the following file failed:
  'my-vignette.Rmd'

Execution halted

* checking PDF version of manual ... [16s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs