* using log directory 'd:/RCompile/CRANincoming/R-devel/LorMe.Rcheck'
* using R Under development (unstable) (2024-08-16 r87026 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 'LorMe/DESCRIPTION' ... OK
* this is package 'LorMe' version '1.0.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'LorMe' can be installed ... WARNING
Found the following significant warnings:
  Warning: D:/temp/RtmpUXsP0A/R.INSTALL2dc8c37b040c7/LorMe/man/tax_summary.Rd:32: unknown macro '\item'
  Warning: D:/temp/RtmpUXsP0A/R.INSTALL2dc8c37b040c7/LorMe/man/tax_summary.Rd:34: unexpected section header '\value'
  Warning: D:/temp/RtmpUXsP0A/R.INSTALL2dc8c37b040c7/LorMe/man/tax_summary.Rd:37: unexpected section header '\description'
  Warning: D:/temp/RtmpUXsP0A/R.INSTALL2dc8c37b040c7/LorMe/man/tax_summary.Rd:40: unexpected section header '\note'
  Warning: D:/temp/RtmpUXsP0A/R.INSTALL2dc8c37b040c7/LorMe/man/tax_summary.Rd:43: unexpected section header '\examples'
  Warning: D:/temp/RtmpUXsP0A/R.INSTALL2dc8c37b040c7/LorMe/man/tax_summary.Rd:87: unexpected section header '\author'
  Warning: D:/temp/RtmpUXsP0A/R.INSTALL2dc8c37b040c7/LorMe/man/tax_summary.Rd:90: unexpected END_OF_INPUT '
See 'd:/RCompile/CRANincoming/R-devel/LorMe.Rcheck/00install.out' for details.
* checking installed package size ... 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 ... 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 ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [112s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                  user system elapsed
manhattan        23.36   0.42   23.78
network_withdiff 13.64   0.42   14.06
Deseq_analysis   10.12   0.71   10.85
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs