* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SMAHP.Rcheck’
* using R Under development (unstable) (2025-03-06 r87893)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* 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 ... [3s/4s] 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 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 ‘SMAHP’ can be installed ... [4s/4s] 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 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 ... [7s/7s] 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 ... [0s/0s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [563s/563s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
StepThree       62.566  0.056  62.640
get_adjusted_p  62.544  0.009  62.569
get_coef        62.456  0.004  62.487
SMAHP           62.297  0.096  62.409
StepTwo         62.361  0.008  62.384
StepOne         62.007  0.048  62.068
get_sig_pathway 61.670  0.004  61.692
get_raw_p       61.391  0.000  61.402
get_pairs       61.312  0.000  61.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [65s/65s] OK
  Running ‘testthat.R’ [65s/65s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [65s/66s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 4 NOTEs