* using log directory ‘/srv/hornik/tmp/CRAN_pretest/gclink.Rcheck’
* using R Under development (unstable) (2025-07-31 r88477)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* checking for file ‘gclink/DESCRIPTION’ ... OK
* this is package ‘gclink’ version ‘1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Liuyang Li <cyanobacteria@yeah.net>’

New submission

Possibly misspelled words in DESCRIPTION:
  BLASTp (14:19)
  Canniffe (20:58)
  EggNOG (14:47)
  FASTA (19:9)
  Hu (20:34)
  Myxococcota (21:27)
  ORFs (15:12, 16:20)
  Rudling (20:42)
  capsid (12:77)
  carotenoid (12:37)
  integrase (13:17)
  polymerase (13:5)
  transcriptomes (13:56)

The Description field contains
  "https://doi.org/10.1038/s41467-023-42193-7".
Please write DOIs as <doi:prefix/suffix>.
* 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 ‘gclink’ can be installed ... [2s/2s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] 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 ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [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 ... [4s/4s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) orf_locate.Rd:19: Lost braces; missing escapes or markup?
    19 | {Biostrings::readBStringSet(., format="fasta", nrec=-1L, skip=0L, seek.first.rec=FALSE, use.names=TRUE)} \%>\%
       | ^
checkRd: (-1) orf_locate.Rd:20: Lost braces; missing escapes or markup?
    20 | {data.frame(Sequence = .)} \%>\%
       | ^
checkRd: (-1) orf_locate.Rd:21: Lost braces; missing escapes or markup?
    21 | {tibble::rownames_to_column(., "SeqName")}
       | ^
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [2s/2s] OK
* checking PDF version of manual ... [4s/3s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ≤ (U+2264)
               not set up for use with LaTeX.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘gclink-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs