* using log directory ‘/srv/hornik/tmp/CRAN_pretest/gap.Rcheck’
* using R Under development (unstable) (2026-02-03 r89375)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1+b1)
    Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-02-04 14:05:52 UTC
* checking for file ‘gap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gap’ version ‘1.7’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/125s] NOTE
Maintainer: ‘Jing Hua Zhao <jinghuazhao@hotmail.com>’

Found the following (possibly) invalid URLs:
  URL: http://CRAN.R-project.org/
    From: inst/doc/jss.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: http://CRAN.R-project.org/doc/Rnews/
    From: inst/doc/jss.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
    From: inst/doc/jss.pdf
    Status: 400
    Message: Bad Request
  URL: http://rgenetics.org/
    From: inst/doc/jss.pdf
    Status: 503
    Message: Service Unavailable
  URL: http://web.inter.nl.net/users/S.van.Buuren/mi/hmtl/mice.htm
    From: inst/doc/jss.pdf
    Status: Error
    Message: Timeout was reached [web.inter.nl.net]:
      Connection timed out after 60001 milliseconds
  URL: http://www.bioconductor.org/ (moved to https://www.bioconductor.org/)
    From: inst/doc/jss.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://www.fnih.org/GAIN2/home_new.shtml (moved to https://fnih.org/GAIN2/home_new.shtml)
    From: inst/doc/jss.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://www.graphviz.org/ (moved to https://www.graphviz.org/)
    From: inst/doc/jss.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://www.hapmap.org/
    From: inst/doc/jss.pdf
    Status: Error
    Message: Could not resolve hostname [www.hapmap.org]:
      Could not resolve host: www.hapmap.org
  URL: http://www.illumina.com/ (moved to https://www.illumina.com:443/)
    From: inst/doc/jss.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://www.sas.com/ (moved to https://www.sas.com/)
    From: inst/doc/jss.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://www.srl.cam.ac.uk/epic/
    From: inst/doc/jss.pdf
    Status: Error
    Message: Timeout was reached [www.srl.cam.ac.uk]:
      Connection timed out after 60001 milliseconds
  URL: http://www.stat.psu.edu/~jls/misoftwa.html (moved to https://science.psu.edu:443/stat)
    From: inst/doc/jss.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://www.wtccc.org.uk/ (moved to https://www.wtccc.org.uk/)
    From: inst/doc/jss.pdf
    Status: 301
    Message: Moved Permanently
  URL: https://doi.org/10.18637/jss.v000.i00
    From: inst/doc/jss.pdf
    Status: 404
    Message: Not Found
  URL: https://www.amazon.com/dp/0126913609/
    From: man/b2r.Rd
    Status: 500
    Message: Internal Server Error
  URL: https://www.amazon.com/dp/0470689285/
    From: man/muvar.Rd
    Status: 500
    Message: Internal Server Error
  URL: https://www.amazon.com/dp/7111109457/
    From: man/b2r.Rd
          man/qqunif.Rd
    Status: 500
    Message: Internal Server Error
  URL: https://www.amazon.com/dp/B011SJAWXG/ (moved to https://www.amazon.com/Statistical-Distributions-Balakrishnan-Nevzorov-Hardcover/dp/B011SJAWXG)
    From: man/qqunif.Rd
    Status: 301
    Message: Moved Permanently
  URL: https://www.amazon.com/dp/B01A0BLZKM/
    From: man/qqfun.Rd
          man/qqunif.Rd
    Status: 500
    Message: Internal Server Error
  URL: https://www.foastat.org/
    From: inst/doc/jss.pdf
    Status: Error
    Message: SSL peer certificate or SSH remote key was not OK [www.foastat.org]:
      SSL certificate verification failed: certificate has expired. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none)
Canonical CRAN.R-project.org URLs use https.
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 ‘gap’ can be installed ... [12s/12s] OK
* used C compiler: ‘Debian clang version 21.1.8 (1+b1)’
* used Fortran compiler: ‘Debian flang version 21.1.8 (1+b1)’
* 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 ... [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 whether startup messages can be suppressed ... [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 ... [13s/13s] OK
* checking Rd files ... [1s/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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking usage of KIND in Fortran files ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in ‘demo’ ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [56s/58s] OK
* checking PDF version of manual ... [5s/5s] OK
* checking HTML version of manual ... [5s/5s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE