* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PSweight.Rcheck’
* using R Under development (unstable) (2025-02-11 r87713)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PSweight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PSweight’ version ‘2.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Yukang Zeng <yukang.zeng@yale.edu>’

Package has a VignetteBuilder field but no prebuilt vignette index.
* 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 ‘PSweight’ can be installed ... [8s/8s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘cran-comments.md’
* 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 ... [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 ... [2s/2s] 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 ... [16s/16s] NOTE
PSmethod_SW: no visible global function definition for ‘quasibinomial’
binest_SW: no visible global function definition for ‘update’
Undefined global functions or variables:
  quasibinomial update
Consider adding
  importFrom("stats", "quasibinomial", "update")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'OUTmethod_SW.Rd':
  \examples lines wider than 100 characters:
     outfit <- OUTmethod_SW(out.formula = out.formula, y=y, datain = datain, dataout = psdata_bin_retrospective_fp)

Rd file 'PSmethod_SW.Rd':
  \examples lines wider than 100 characters:
     psfit <- PSmethod_SW(ps.formula = ps.formula,data = psdata_bin_retrospective_fp, survey.weight = survey.weight, ncate=2)

Rd file 'PSweight_SW.Rd':
  \examples lines wider than 100 characters:
     pato1_sw <- PSweight_SW(ps.formula = ps.formula, yname = "Y", data = psdata_bin_prospective_fp, weight = "overlap", 
                             survey.indicator = TRUE, survey.design = "Prospective", svywtname = "survey_weight", 
                             out.formula = NULL, out.estimate = NULL, family = "gaussian", ps.method = "glm", 
     # Example 2: Retrospective design with augmentation using the Weighted Regression Estimator(WET) estimator
     pato2_sw <- PSweight_SW(ps.formula = ps.formula, yname = "Y", data = psdata_bin_retrospective_fp, weight = "overlap", 
                             survey.indicator = TRUE, survey.design = "Retrospective", svywtname = "survey_weight", 
                             delta = 0.1, augmentation = TRUE, augmentation.type = "WET", bootstrap = FALSE, R = 50, 
                             out.formula = out.formula, out.estimate = NULL, family = "gaussian", ps.method = "glm", 

Rd file 'SumStat_SW.Rd':
  \examples lines wider than 100 characters:
                                survey.indicator = TRUE, svywtname = "survey_weight", survey.design = "Prospective")
     sumstat_retro <- SumStat_SW(ps.formula = ps.formula, trtgrp = "2", data = psdata_bin_retrospective_fp,
                                survey.indicator = TRUE, svywtname = "survey_weight", survey.design = "Retrospective")

Rd file 'plot.SumStat_SW.Rd':
  \examples lines wider than 100 characters:
                          survey.indicator = TRUE, svywtname = "survey_weight", survey.design = "Prospective")

These lines will be truncated in the PDF manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Software_vig.pdf’
* checking examples ... [7s/7s] OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [4s/4s] 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: 1 WARNING, 5 NOTEs