* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/preseqR.Rcheck’
* using R Under development (unstable) (2025-07-15 r88411)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-19) 14.2.0
    GNU Fortran (Debian 14.2.0-19) 14.2.0
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* checking for file ‘preseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘preseqR’ version ‘4.0.0’
* checking CRAN incoming feasibility ... [1s/1s] NOTE
Maintainer: ‘Chao Deng <chaodeng@usc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chao",
                      family = "Deng",
                      role = c("aut", "cre"),
                      email = "chaodeng@usc.edu"),
               person(given = "Timothy",
                      family = "Daley",
                      role = "aut"),
               person(given = c("Andrew", "D."),
                      family = "Smith",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  Deng C, et al. (2018) <arXiv:1607.02804v3>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘bbc.rSAC.Rd’:
    \keyword{ estimator, r-SAC, nonparametric }
  File ‘cs.rSAC.Rd’:
    \keyword{ estimator, r-SAC, nonparametric }
  File ‘ds.rSAC.Rd’:
    \keyword{ estimator, r-SAC, RFA, nonparametric}
  File ‘ds.rSAC.bootsrap.Rd’:
    \keyword{ estimator, r-SAC, RFA, bootstrap, nonpar [TRUNCATED]
  File ‘fisher.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric }
  File ‘kmer.frac.curve.Rd’:
    \keyword{k-mer, sample coverage, high-throughput,  [TRUNCATED]
  File ‘kmer.frac.curve.bootstrap.Rd’:
    \keyword{k-mer, sample coverage, bootstrap, high-t [TRUNCATED]
  File ‘preseqR.interpolate.rSAC.Rd’:
    \keyword{ interpolation, r-SAC}
  File ‘preseqR.optimal.sequencing.Rd’:
    \keyword{WGS, high-throughput, benefit-cost ratio} [TRUNCATED]
  File ‘preseqR.rSAC.Rd’:
    \keyword{ estimator, r-SAC, RFA, ZTNB, best practi [TRUNCATED]
  File ‘preseqR.rSAC.bootstrap.Rd’:
    \keyword{ estimator, r-SAC, bootstrap, best practi [TRUNCATED]
  File ‘preseqR.rSAC.sequencing.rmdup.Rd’:
    \keyword{r-SAC, duplicates, WES, WGS, high-through [TRUNCATED]
  File ‘preseqR.sample.cov.Rd’:
    \keyword{ estimator, RFA, sample coverage}
  File ‘preseqR.sample.cov.bootstrap.Rd’:
    \keyword{ estimator, RFA, bootstrap, sample covera [TRUNCATED]
  File ‘preseqR.simu.hist.Rd’:
    \keyword{ simulation, sampling, mixture of Poisson [TRUNCATED]
  File ‘preseqR.ztnb.em.Rd’:
    \keyword{ negative binomial, EM}
  File ‘ztnb.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric, negative b [TRUNCATED]
  File ‘ztp.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric, Poisson}
* 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 serialization versions ... OK
* checking whether package ‘preseqR’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/preseqR-00install.html' for details.
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [5s/7s] OK
* checking Rd files ... [0s/1s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... [4s/5s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE