• using R Under development (unstable) (2024-09-07 r87105 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 13.2.0     GNU Fortran (GCC) 13.2.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'bigsnpr/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'bigsnpr' version '1.12.2'
• package encoding: UTF-8
• 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 whether package 'bigsnpr' can be installed ... OK See the install log for details.
• used C++ compiler: 'g++.exe (GCC) 13.2.0'
• checking installed package size ... OK
• checking package 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 ... [3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s] OK
• checking whether the package can be unloaded cleanly ... [2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s] OK
• checking whether the namespace can be unloaded cleanly ... [3s] OK
• checking loading without being on the library search path ... [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 ... [11s] OK
• checking Rd files ... [2s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   LDpred2.Rd: SFBM-class, nb_cores   SCT.Rd: FBM.code256-class, nb_cores, big_spLogReg, big_spLinReg   bed_MAF.Rd: nb_cores   bed_counts.Rd: nb_cores   bed_cprodVec.Rd: nb_cores   bed_prodVec.Rd: nb_cores   bed_projectPCA.Rd: as_scaling_fun, nb_cores   bed_projectSelfPCA.Rd: nb_cores   bed_randomSVD.Rd: nb_cores   bed_scaleBinom.Rd: nb_cores   bed_tcrossprodSelf.Rd: as_scaling_fun   bigSNP-class.Rd: FBM.code256-class   bigsnpr-package.Rd: FBM.code256-class, nb_cores   snp_MAF.Rd: FBM.code256-class, nb_cores   snp_MAX3.Rd: FBM.code256-class   snp_PRS.Rd: FBM.code256-class, big_univLinReg, big_univLogReg   snp_asGeneticPos.Rd: nb_cores   snp_autoSVD.Rd: FBM.code256-class, as_scaling_fun, nb_cores   snp_beagleImpute.Rd: nb_cores   snp_clumping.Rd: nb_cores, FBM.code256-class   snp_cor.Rd: FBM.code256-class, nb_cores   snp_fastImpute.Rd: FBM.code256-class, nb_cores, FBM   snp_fastImputeSimple.Rd: FBM.code256-class, nb_cores   snp_gc.Rd: big_univLinReg, big_univLogReg   snp_lassosum2.Rd: SFBM-class, nb_cores   snp_ld_scores.Rd: FBM.code256-class, nb_cores   snp_ldsc.Rd: nb_cores, SFBM-class   snp_manhattan.Rd: big_univLinReg, big_univLogReg   snp_pcadapt.Rd: FBM.code256-class, nb_cores   snp_plinkIBDQC.Rd: nb_cores   snp_plinkKINGQC.Rd: nb_cores   snp_prodBGEN.Rd: nb_cores   snp_qq.Rd: big_univLinReg, big_univLogReg   snp_readBGEN.Rd: nb_cores   snp_readBed.Rd: nb_cores   snp_simuPheno.Rd: FBM.code256-class, nb_cores   snp_split.Rd: FBM.code256-class, foreach, nb_cores Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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] 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 pragmas in C/C++ headers and code ... OK
• checking compiled code ... OK
• checking examples ... [51s] OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [132s] OK   Running 'spelling.R' [0s]   Running 'testthat.R' [131s]
• checking PDF version of manual ... [24s] OK
• checking HTML version of manual ... [13s] NOTE Found the following HTML validation problems: snp_ldsc.html:134:1 (snp_ldsc.Rd:74): Warning: trimming empty <dt>
• DONE

Status: 2 NOTEs