* using log directory ‘/srv/hornik/tmp/CRAN/LorMe.Rcheck’
* using R Under development (unstable) (2024-08-16 r87026)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘LorMe/DESCRIPTION’ ... OK
* this is package ‘LorMe’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Ningqi Wang <2434066068@qq.com>’

New submission
* 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 ‘LorMe’ can be installed ... [11s/11s] WARNING
Found the following significant warnings:
  Warning: /srv/hornik/tmp/CRAN/LorMe.Rcheck/00_pkg_src/LorMe/man/tax_summary.Rd:32: unknown macro '\item'
  Warning: /srv/hornik/tmp/CRAN/LorMe.Rcheck/00_pkg_src/LorMe/man/tax_summary.Rd:34: unexpected section header '\value'
  Warning: /srv/hornik/tmp/CRAN/LorMe.Rcheck/00_pkg_src/LorMe/man/tax_summary.Rd:37: unexpected section header '\description'
  Warning: /srv/hornik/tmp/CRAN/LorMe.Rcheck/00_pkg_src/LorMe/man/tax_summary.Rd:40: unexpected section header '\note'
  Warning: /srv/hornik/tmp/CRAN/LorMe.Rcheck/00_pkg_src/LorMe/man/tax_summary.Rd:43: unexpected section header '\examples'
  Warning: /srv/hornik/tmp/CRAN/LorMe.Rcheck/00_pkg_src/LorMe/man/tax_summary.Rd:87: unexpected section header '\author'
  Warning: /srv/hornik/tmp/CRAN/LorMe.Rcheck/00_pkg_src/LorMe/man/tax_summary.Rd:90: unexpected END_OF_INPUT '
See ‘/srv/hornik/tmp/CRAN/LorMe.Rcheck/00install.out’ for details.
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [15s/15s] OK
* checking Rd files ... [0s/0s] WARNING
prepare_Rd: ./man/tax_summary.Rd:32: unknown macro '\item'
prepare_Rd: ./man/tax_summary.Rd:34: unexpected section header '\value'
prepare_Rd: ./man/tax_summary.Rd:37: unexpected section header '\description'
prepare_Rd: ./man/tax_summary.Rd:40: unexpected section header '\note'
prepare_Rd: ./man/tax_summary.Rd:43: unexpected section header '\examples'
prepare_Rd: ./man/tax_summary.Rd:87: unexpected section header '\author'
prepare_Rd: ./man/tax_summary.Rd:90: unexpected END_OF_INPUT '
'
checkRd: (-1) tax_summary.Rd:32: Lost braces
    32 | \item{outputtax}{Names of output taxonomy level table.Default:c("Phylum","Genus"). Shortcut input is available with 'standard' and 'complete' same as above.}
       |      ^
checkRd: (-1) tax_summary.Rd:32: Lost braces
    32 | \item{outputtax}{Names of output taxonomy level table.Default:c("Phylum","Genus"). Shortcut input is available with 'standard' and 'complete' same as above.}
       |                 ^
checkRd: (-1) tax_summary.Rd:34-36: Lost braces
    34 | \value{
       |       ^
checkRd: (-1) tax_summary.Rd:37-39: Lost braces
    37 | \description{
       |             ^
checkRd: (-1) tax_summary.Rd:40-42: Lost braces
    40 | \note{
       |      ^
checkRd: (-1) tax_summary.Rd:43-86: Lost braces
    43 | \examples{
       |          ^
checkRd: (-1) tax_summary.Rd:87-89: Lost braces
    87 | \author{
       |        ^
* 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 ... WARNING
Undocumented arguments in Rd file 'tax_summary.Rd'
  ‘outputtax’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Rd files without \description:
  ‘tax_summary.Rd’
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [97s/101s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
manhattan        19.146  0.100  19.246
network_withdiff 12.833  0.040  12.872
Deseq_analysis   10.151  0.464  10.618
Deseq_analysis2   5.242  0.044   5.287
* 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: 3 WARNINGs, 3 NOTEs