* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MAGEE.Rcheck’
* using R Under development (unstable) (2026-02-10 r89394)
* 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: 2026-02-11 23:37:45 UTC
* checking for file ‘MAGEE/DESCRIPTION’ ... OK
* this is package ‘MAGEE’ version ‘1.4.5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Han Chen <hanchenphd@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: http://bioconductor.org/packages/release/bioc/html/SeqArray.html (moved to https://bioconductor.org/packages/release/bioc/html/SeqArray.html)
    From: inst/doc/MAGEE.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://bioconductor.org/packages/release/bioc/html/SeqVarTools.html (moved to https://bioconductor.org/packages/release/bioc/html/SeqVarTools.html)
    From: inst/doc/MAGEE.pdf
    Status: 301
    Message: Moved Permanently
  URL: http://zzz.bwh.harvard.edu/plink/data.shtml#bed
    From: inst/doc/MAGEE.pdf
    Status: Error
    Message: SSL peer certificate or SSH remote key was not OK [zzz.bwh.harvard.edu]:
      SSL certificate verification failed: certificate has expired. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none)
  URL: https://cran.r-project.org/web/packages/CompQuadForm/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/GMMAT/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/GMMAT/vignettes/GMMAT.pdf
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/Matrix/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/Rcpp/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/RcppArmadillo/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/RhpcBLASctl/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/data.table/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/doMC/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/foreach/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/testthat/index.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/views/HighPerformanceComputing.html
    From: inst/doc/MAGEE.pdf
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://software.intel.com/en-us/articles/using-intel-mkl-with-r (moved to https://www.intel.com/content/www/us/en/developer/articles/technical/using-onemkl-with-r.html)
    From: inst/doc/MAGEE.pdf
    Status: 301
    Message: Moved Permanently
The canonical URL of the CRAN page for a package is 
  https://CRAN.R-project.org/package=pkgname
The canonical URL of the CRAN page for a task view is 
  https://CRAN.R-project.org/view=viewname
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 ‘MAGEE’ can be installed ... [30s/30s] OK
* used C compiler: ‘Debian clang version 21.1.8 (3)’
* used C++ compiler: ‘Debian clang version 21.1.8 (3)’
* 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 ... [13s/13s] OK
* checking Rd files ... [0s/0s] 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 line endings in shell scripts ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [33s/33s] OK
  Running ‘testthat.R’ [33s/33s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [3s/3s] OK
* checking PDF version of manual ... [3s/3s] 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 NOTE