* using log directory 'd:/RCompile/CRANincoming/R-devel/SMAHP.Rcheck'
* using R Under development (unstable) (2025-03-05 r87891 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'SMAHP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SMAHP' version '0.0.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Weijia Fu <weijia.fu@mountsinai.org>'

New submission

Possibly misspelled words in DESCRIPTION:
  Omics (3:16)
  Proteogenomic (4:26)
  SMAHP (15:25)
  omics (15:166)
* 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 'SMAHP' 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 ... NOTE
SIS_combo: no visible binding for global variable 'effect'
StepTwo: no visible binding for global variable 'effect'
Undefined global functions or variables:
  effect
* checking Rd files ... NOTE
checkRd: (-1) SMAHP.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SMAHP.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SMAHP.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SMAHP.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SMAHP.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StepOne.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StepOne.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StepOne.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StepThree.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StepThree.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StepThree.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StepThree.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_coef.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_coef.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_coef.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
* 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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [491s] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                 user system elapsed
get_pairs       57.98   0.20   58.19
get_raw_p       57.75   0.17   57.92
get_coef        57.33   0.46   57.78
SMAHP           57.38   0.27   57.64
StepOne         56.54   0.18   56.75
get_sig_pathway 53.92   0.37   54.29
get_adjusted_p  52.84   0.18   53.03
StepTwo         45.75   0.15   45.90
StepThree       44.42   0.13   44.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [54s] OK
  Running 'testthat.R' [54s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [61s] OK
* checking PDF version of manual ... [12s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 NOTEs