* using log directory 'd:/RCompile/CRANincoming/R-devel/PQLseq.Rcheck'
* using R Under development (unstable) (2025-11-06 r88990 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'PQLseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PQLseq' version '1.22'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Jiaqiang Zhu <jiaqiang@umich.edu>'

Version jumps in minor (submitted: 1.22, existing: 1.2.1)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Shiquan",
                      family = "Sun",
                      role = "aut"),
               person(given = "Jiaqiang",
                      family = "Zhu",
                      role = c("aut", "cre"),
                      email = "jiaqiang@umich.edu"),
               person(given = "Xiang",
                      family = "Zhou",
                      role = "aut"))
as necessary.
* 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 serialization versions ... OK
* checking whether package 'PQLseq' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.3.0'
* 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 ... [10s] NOTE
Found if() conditions comparing class() to string:
File 'PQLseq/R/PQLseq.R': if (!is.null(model1) & (class(model1) != "try-error")) ...
File 'PQLseq/R/PQLseq.R': if (class(model1) != "try-error" & !is.null(model1)) ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in 'PQLseq-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ExampleBSseq
> ### Title: BSseq example dataset
> ### Aliases: ExampleBSseq
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ExampleBSseq)
> attach(ExampleBSseq)
> model_DNA=pqlseq(RawCountDataSet=mcount, Phenotypes=predictor, 
+   RelatednessMatrix=relatednessmatrix, LibSize=totalcount,
+   fit.model="BMM",numCore=1)
## number of total individuals:  100 
## number of total genes/sites:  5 
## number of adjusted covariates:  0 
# fitting binomial mixed model ... 
> head(model_DNA)
      numIDV        beta    se_beta     pvalue        h2    sigma2 converged
site1    100 -0.01522828 0.04427932 0.73091092 0.1988914 0.8919006      TRUE
site2     96  0.02303264 0.04412310 0.60166432 0.2011540 0.6403068      TRUE
site3    100 -0.10590054 0.04727553 0.02508631 0.8664968 0.6315116      TRUE
site4     98  0.01511581 0.04498207 0.73684018 0.4913475 0.8255169      TRUE
site5    100 -0.03719854 0.04670410 0.42575739 0.0000000 1.2851617      TRUE
> detach(ExampleBSseq)
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("ExampleBSseq", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
Error: connections left open:
	<-CRANwin3.fb05.statistik.uni-dortmund.de:11528 (sockconn)
Execution halted
* checking PDF version of manual ... [26s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs