* using log directory ‘/home/hornik/tmp/CRAN_recheck/bigsnpr.Rcheck’
* using R Under development (unstable) (2024-11-25 r87381)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-1) 14.2.0
    GNU Fortran (Debian 14.2.0-1) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘bigsnpr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigsnpr’ version ‘1.12.18’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [8s/9s] NOTE
Maintainer: ‘Florian Privé <florian.prive.21@gmail.com>’

Found the following (possibly) invalid URLs:
  URL: https://genome.sph.umich.edu/wiki/Regions_of_high_linkage_disequilibrium_(LD)
    From: man/LD.wiki34.Rd
    Status: Error
    Message: server verification failed: certificate signer not trusted. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none)
* 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 ‘bigsnpr’ can be installed ... [97s/97s] OK
* used C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
* 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 ... [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 ... [2s/2s] 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 ... [12s/12s] 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 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 ... [39s/41s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
snp_clumping 7.248  0.003   7.255
snp_autoSVD  6.472  0.040   6.877
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [134s/146s] OK
  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [134s/145s]
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs