• using R Under development (unstable) (2024-09-04 r87094)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 18.1.8 (9)     Debian flang-new version 18.1.8 (9)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘statgenGWAS/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘statgenGWAS’ version ‘1.0.9’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘statgenGWAS’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 18.1.8 (9)’
• checking C++ specification ... NOTE   Specified C++11: please drop specification unless essential
• 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 ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/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 ... [11s/14s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   runSingleTraitGwas.Rd: GWAS 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 ... [2s/3s] OK
• checking LazyData ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/6s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [13s/18s] ERROR   Running ‘tinytest.R’ [13s/17s] Running the tests in ‘tests/tinytest.R’ failed. Complete output:   >   > if ( requireNamespace("tinytest", quietly=TRUE) ){   + tinytest::test_package("statgenGWAS")   + }      test_GWAS.R................... 0 tests   test_GWAS.R................... 0 tests   test_GWAS.R................... 0 tests   test_GWAS.R................... 0 tests   test_GWAS.R................... 1 tests [0;32mOK [0m   test_GWAS.R................... 2 tests [0;32mOK [0m   test_GWAS.R................... 2 tests [0;32mOK [0m   test_GWAS.R................... 3 tests [0;32mOK [0m   test_GWAS.R................... 4 tests [0;32mOK [0m   test_GWAS.R................... 5 tests [0;32mOK [0m   test_GWAS.R................... 6 tests [0;32mOK [0m   test_GWAS.R................... 7 tests [0;32mOK [0m   test_GWAS.R................... 8 tests [0;32mOK [0m   test_GWAS.R................... 9 tests [0;32mOK [0m   test_GWAS.R................... 10 tests [0;32mOK [0m   test_GWAS.R................... 11 tests [0;32mOK [0m   test_GWAS.R................... 11 tests [0;32mOK [0m   test_GWAS.R................... 12 tests [0;32mOK [0m   test_GWAS.R................... 13 tests [0;32mOK [0m   test_GWAS.R................... 14 tests [0;32mOK [0m   test_GWAS.R................... 15 tests [0;32mOK [0m   test_GWAS.R................... 15 tests [0;32mOK [0m   test_GWAS.R................... 16 tests [0;32mOK [0m   test_GWAS.R................... 17 tests [0;32mOK [0m [0;34m0.4s [0m      test_STG.R.................... 0 tests   test_STG.R.................... 0 tests   test_STG.R.................... 0 tests   test_STG.R.................... 0 tests   test_STG.R.................... 0 tests   test_STG.R.................... 0 tests   test_STG.R.................... 0 tests   test_STG.R.................... 0 tests   test_STG.R.................... 1 tests [0;32mOK [0m   test_STG.R.................... 2 tests [0;32mOK [0m   test_STG.R.................... 3 tests [0;32mOK [0m   test_STG.R.................... 4 tests [0;32mOK [0m   test_STG.R.................... 5 tests [0;32mOK [0m   test_STG.R.................... 6 tests [0;32mOK [0m   test_STG.R.................... 7 tests [0;32mOK [0m   test_STG.R.................... 8 tests [0;32mOK [0m   test_STG.R.................... 9 tests [0;32mOK [0m   test_STG.R.................... 10 tests [0;32mOK [0m   test_STG.R.................... 11 tests [0;32mOK [0m   test_STG.R.................... 12 tests [0;32mOK [0m   test_STG.R.................... 13 tests [0;32mOK [0m   test_STG.R.................... 14 tests [0;32mOK [0m   test_STG.R.................... 15 tests [0;32mOK [0m   test_STG.R.................... 16 tests [0;32mOK [0m   test_STG.R.................... 17 tests [0;32mOK [0m   test_STG.R.................... 17 tests [0;32mOK [0m   test_STG.R.................... 17 tests [0;32mOK [0m   test_STG.R.................... 17 tests [0;32mOK [0m   test_STG.R.................... 17 tests [0;32mOK [0m   test_STG.R.................... 17 tests [0;32mOK [0m   test_STG.R.................... 18 tests [0;32mOK [0m   test_STG.R.................... 19 tests [0;32mOK [0m   test_STG.R.................... 20 tests [0;32mOK [0m   test_STG.R.................... 21 tests [0;32mOK [0m   test_STG.R.................... 22 tests [0;32mOK [0m   test_STG.R.................... 23 tests [0;32mOK [0m   test_STG.R.................... 24 tests [0;32mOK [0m   test_STG.R.................... 25 tests [0;32mOK [0m   test_STG.R.................... 26 tests [0;32mOK [0m   test_STG.R.................... 27 tests [0;32mOK [0m   test_STG.R.................... 28 tests [0;32mOK [0m   test_STG.R.................... 29 tests [0;32mOK [0m   test_STG.R.................... 30 tests [0;32mOK [0m   test_STG.R.................... 31 tests [0;32mOK [0m   test_STG.R.................... 32 tests [0;32mOK [0m   test_STG.R.................... 33 tests [0;32mOK [0m   test_STG.R.................... 34 tests [0;32mOK [0m   test_STG.R.................... 35 tests [0;32mOK [0m   test_STG.R.................... 36 tests [0;32mOK [0m   test_STG.R.................... 37 tests [0;32mOK [0m [0;34m1.5s [0m      test_STGHelper.R.............. 0 tests   test_STGHelper.R.............. 0 tests   test_STGHelper.R.............. 0 tests   test_STGHelper.R.............. 1 tests [0;32mOK [0m   test_STGHelper.R.............. 2 tests [0;32mOK [0m   test_STGHelper.R.............. 3 tests [0;32mOK [0m   test_STGHelper.R.............. 3 tests [0;32mOK [0m   test_STGHelper.R.............. 4 tests [0;32mOK [0m   test_STGHelper.R.............. 5 tests [0;32mOK [0m   test_STGHelper.R.............. 6 tests [0;32mOK [0m   test_STGHelper.R.............. 7 tests [0;32mOK [0m   test_STGHelper.R.............. 8 tests [0;32mOK [0m   test_STGHelper.R.............. 9 tests [0;32mOK [0m   test_STGHelper.R.............. 10 tests [0;32mOK [0m   test_STGHelper.R.............. 11 tests [0;32mOK [0m   test_STGHelper.R.............. 12 tests [0;32mOK [0m   test_STGHelper.R.............. 13 tests [0;32mOK [0m   test_STGHelper.R.............. 14 tests [0;32mOK [0m   test_STGHelper.R.............. 14 tests [0;32mOK [0m   test_STGHelper.R.............. 15 tests [0;32mOK [0m   test_STGHelper.R.............. 16 tests [0;32mOK [0m   test_STGHelper.R.............. 17 tests [0;32mOK [0m   test_STGHelper.R.............. 18 tests [0;32mOK [0m   test_STGHelper.R.............. 18 tests [0;32mOK [0m   test_STGHelper.R.............. 19 tests [0;32mOK [0m   test_STGHelper.R.............. 20 tests [0;32mOK [0m   test_STGHelper.R.............. 20 tests [0;32mOK [0m   test_STGHelper.R.............. 20 tests [0;32mOK [0m   test_STGHelper.R.............. 21 tests [0;32mOK [0m   test_STGHelper.R.............. 22 tests [0;31m1 fails [0m   test_STGHelper.R.............. 23 tests [0;31m2 fails [0m   test_STGHelper.R.............. 24 tests [0;31m3 fails [0m   test_STGHelper.R.............. 25 tests [0;31m4 fails [0m   test_STGHelper.R.............. 26 tests [0;31m4 fails [0m   test_STGHelper.R.............. 27 tests [0;31m4 fails [0m   test_STGHelper.R.............. 28 tests [0;31m4 fails [0m   test_STGHelper.R.............. 29 tests [0;31m4 fails [0m   test_STGHelper.R.............. 30 tests [0;31m4 fails [0m   test_STGHelper.R.............. 31 tests [0;31m4 fails [0m [0;36m81ms [0m      test_STGoptions.R............. 0 tests   test_STGoptions.R............. 1 tests [0;32mOK [0m   test_STGoptions.R............. 1 tests [0;32mOK [0m   test_STGoptions.R............. 1 tests [0;32mOK [0m   test_STGoptions.R............. 2 tests [0;32mOK [0m   test_STGoptions.R............. 3 tests [0;32mOK [0m   test_STGoptions.R............. 4 tests [0;32mOK [0m   test_STGoptions.R............. 5 tests [0;32mOK [0m   test_STGoptions.R............. 6 tests [0;32mOK [0m   test_STGoptions.R............. 6 tests [0;32mOK [0m   test_STGoptions.R............. 6 tests [0;32mOK [0m   test_STGoptions.R............. 7 tests [0;32mOK [0m   test_STGoptions.R............. 8 tests [0;32mOK [0m   test_STGoptions.R............. 9 tests [0;32mOK [0m   test_STGoptions.R............. 10 tests [0;32mOK [0m   test_STGoptions.R............. 11 tests [0;32mOK [0m   test_STGoptions.R............. 11 tests [0;32mOK [0m   test_STGoptions.R............. 12 tests [0;32mOK [0m   test_STGoptions.R............. 13 tests [0;32mOK [0m   test_STGoptions.R............. 14 tests [0;32mOK [0m   test_STGoptions.R............. 14 tests [0;32mOK [0m   test_STGoptions.R............. 15 tests [0;32mOK [0m   test_STGoptions.R............. 16 tests [0;32mOK [0m   test_STGoptions.R............. 17 tests [0;32mOK [0m   test_STGoptions.R............. 18 tests [0;32mOK [0m   test_STGoptions.R............. 19 tests [0;32mOK [0m   test_STGoptions.R............. 19 tests [0;32mOK [0m   test_STGoptions.R............. 20 tests [0;32mOK [0m   test_STGoptions.R............. 21 tests [0;32mOK [0m   test_STGoptions.R............. 22 tests [0;32mOK [0m   test_STGoptions.R............. 22 tests [0;32mOK [0m   test_STGoptions.R............. 23 tests [0;32mOK [0m   test_STGoptions.R............. 24 tests [0;32mOK [0m [0;34m2.1s [0m      test_chkFuncs.R............... 0 tests   test_chkFuncs.R............... 1 tests [0;32mOK [0m   test_chkFuncs.R............... 2 tests [0;32mOK [0m   test_chkFuncs.R............... 3 tests [0;32mOK [0m   test_chkFuncs.R............... 3 tests [0;32mOK [0m   test_chkFuncs.R............... 3 tests [0;32mOK [0m   test_chkFuncs.R............... 4 tests [0;32mOK [0m   test_chkFuncs.R............... 5 tests [0;32mOK [0m   test_chkFuncs.R............... 6 tests [0;32mOK [0m   test_chkFuncs.R............... 7 tests [0;32mOK [0m   test_chkFuncs.R............... 8 tests [0;32mOK [0m   test_chkFuncs.R............... 9 tests [0;32mOK [0m   test_chkFuncs.R............... 10 tests [0;32mOK [0m   test_chkFuncs.R............... 11 tests [0;32mOK [0m   test_chkFuncs.R............... 12 tests [0;32mOK [0m   test_chkFuncs.R............... 13 tests [0;32mOK [0m   test_chkFuncs.R............... 14 tests [0;32mOK [0m   test_chkFuncs.R............... 15 tests [0;32mOK [0m   test_chkFuncs.R............... 16 tests [0;32mOK [0m   test_chkFuncs.R............... 17 tests [0;32mOK [0m   test_chkFuncs.R............... 18 tests [0;32mOK [0m   test_chkFuncs.R............... 19 tests [0;32mOK [0m   test_chkFuncs.R............... 20 tests [0;32mOK [0m   test_chkFuncs.R............... 21 tests [0;32mOK [0m   test_chkFuncs.R............... 22 tests [0;32mOK [0m   test_chkFuncs.R............... 23 tests [0;32mOK [0m   test_chkFuncs.R............... 24 tests [0;32mOK [0m   test_chkFuncs.R............... 25 tests [0;32mOK [0m   test_chkFuncs.R............... 26 tests [0;32mOK [0m   test_chkFuncs.R............... 27 tests [0;32mOK [0m   test_chkFuncs.R............... 28 tests [0;32mOK [0m   test_chkFuncs.R............... 29 tests [0;32mOK [0m   test_chkFuncs.R............... 30 tests [0;32mOK [0m   test_chkFuncs.R............... 30 tests [0;32mOK [0m   test_chkFuncs.R............... 31 tests [0;32mOK [0m   test_chkFuncs.R............... 31 tests [0;32mOK [0m   test_chkFuncs.R............... 32 tests [0;32mOK [0m   test_chkFuncs.R............... 33 tests [0;32mOK [0m   test_chkFuncs.R............... 34 tests [0;32mOK [0m   test_chkFuncs.R............... 35 tests [0;32mOK [0m   test_chkFuncs.R............... 36 tests [0;32mOK [0m   test_chkFuncs.R............... 37 tests [0;32mOK [0m   test_chkFuncs.R............... 38 tests [0;32mOK [0m   test_chkFuncs.R............... 39 tests [0;32mOK [0m   test_chkFuncs.R............... 40 tests [0;32mOK [0m   test_chkFuncs.R............... 41 tests [0;32mOK [0m   test_chkFuncs.R............... 42 tests [0;32mOK [0m   test_chkFuncs.R............... 43 tests [0;32mOK [0m [0;36m25ms [0m      test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 0 tests   test_codeMarkers.R............ 1 tests [0;32mOK [0m   test_codeMarkers.R............ 2 tests [0;32mOK [0m   test_codeMarkers.R............ 3 tests [0;32mOK [0m   test_codeMarkers.R............ 4 tests [0;32mOK [0m   test_codeMarkers.R............ 5 tests [0;32mOK [0m   test_codeMarkers.R............ 6 tests [0;32mOK [0m   test_codeMarkers.R............ 7 tests [0;32mOK [0m   test_codeMarkers.R............ 8 tests [0;32mOK [0m   test_codeMarkers.R............ 9 tests [0;32mOK [0m   test_codeMarkers.R............ 10 tests [0;32mOK [0m   test_codeMarkers.R............ 11 tests [0;32mOK [0m   test_codeMarkers.R............ 12 tests [0;32mOK [0m   test_codeMarkers.R............ 13 tests [0;32mOK [0m   test_codeMarkers.R............ 14 tests [0;32mOK [0m   test_codeMarkers.R............ 14 tests [0;32mOK [0m   test_codeMarkers.R............ 15 tests [0;32mOK [0m   test_codeMarkers.R............ 16 tests [0;32mOK [0m   test_codeMarkers.R............ 17 tests [0;32mOK [0m   test_codeMarkers.R............ 18 tests [0;32mOK [0m   test_codeMarkers.R............ 19 tests [0;32mOK [0m   test_codeMarkers.R............ 19 tests [0;32mOK [0m   test_codeMarkers.R............ 19 tests [0;32mOK [0m   test_codeMarkers.R............ 20 tests [0;32mOK [0m   test_codeMarkers.R............ 21 tests [0;32mOK [0m   test_codeMarkers.R............ 22 tests [0;32mOK [0m   test_codeMarkers.R............ 23 tests [0;32mOK [0m   test_codeMarkers.R............ 24 tests [0;32mOK [0m   test_codeMarkers.R............ 25 tests [0;32mOK [0m   test_codeMarkers.R............ 26 tests [0;32mOK [0m   test_codeMarkers.R............ 27 tests [0;32mOK [0m   test_codeMarkers.R............ 28 tests [0;32mOK [0m   test_codeMarkers.R............ 29 tests [0;32mOK [0m   test_codeMarkers.R............ 30 tests [0;32mOK [0m   test_codeMarkers.R............ 31 tests [0;32mOK [0m   test_codeMarkers.R............ 32 tests [0;32mOK [0m   test_codeMarkers.R............ 33 tests [0;32mOK [0m   test_codeMarkers.R............ 34 tests [0;32mOK [0m   test_codeMarkers.R............ 35 tests [0;32mOK [0m   test_codeMarkers.R............ 36 tests [0;32mOK [0m   test_codeMarkers.R............ 37 tests [0;32mOK [0m   test_codeMarkers.R............ 37 tests [0;32mOK [0m   test_codeMarkers.R............ 37 tests [0;32mOK [0m   test_codeMarkers.R............ 38 tests [0;32mOK [0m   test_codeMarkers.R............ 38 tests [0;32mOK [0m   test_codeMarkers.R............ 38 tests [0;32mOK [0m   test_codeMarkers.R............ 39 tests [0;32mOK [0m   test_codeMarkers.R............ 39 tests [0;32mOK [0m   test_codeMarkers.R............ 40 tests [0;32mOK [0m   test_codeMarkers.R............ 41 tests [0;32mOK [0m   test_codeMarkers.R............ 42 tests [0;32mOK [0m   test_codeMarkers.R............ 43 tests [0;32mOK [0m   test_codeMarkers.R............ 44 tests [0;32mOK [0m [0;36m92ms [0m      test_gData.R.................. 0 tests   test_gData.R.................. 0 tests   test_gData.R.................. 0 tests   test_gData.R.................. 0 tests   test_gData.R.................. 0 tests   test_gData.R.................. 0 tests   test_gData.R.................. 0 tests   test_gData.R.................. 0 tests   test_gData.R.................. 1 tests [0;32mOK [0m   test_gData.R.................. 2 tests [0;32mOK [0m   test_gData.R.................. 3 tests [0;32mOK [0m   test_gData.R.................. 4 tests [0;32mOK [0m   test_gData.R.................. 4 tests [0;32mOK [0m   test_gData.R.................. 4 tests [0;32mOK [0m   test_gData.R.................. 5 tests [0;32mOK [0m   test_gData.R.................. 6 tests [0;32mOK [0m   test_gData.R.................. 6 tests [0;32mOK [0m   test_gData.R.................. 6 tests [0;32mOK [0m   test_gData.R.................. 7 tests [0;32mOK [0m   test_gData.R.................. 8 tests [0;32mOK [0m   test_gData.R.................. 9 tests [0;32mOK [0m   test_gData.R.................. 9 tests [0;32mOK [0m   test_gData.R.................. 10 tests [0;32mOK [0m   test_gData.R.................. 11 tests [0;32mOK [0m   test_gData.R.................. 12 tests [0;32mOK [0m   test_gData.R.................. 13 tests [0;32mOK [0m   test_gData.R.................. 14 tests [0;32mOK [0m   test_gData.R.................. 15 tests [0;32mOK [0m   test_gData.R.................. 16 tests [0;32mOK [0m   test_gData.R.................. 16 tests [0;32mOK [0m   test_gData.R.................. 17 tests [0;32mOK [0m   test_gData.R.................. 17 tests [0;32mOK [0m   test_gData.R.................. 17 tests [0;32mOK [0m   test_gData.R.................. 18 tests [0;32mOK [0m   test_gData.R.................. 19 tests [0;32mOK [0m   test_gData.R.................. 19 tests [0;32mOK [0m   test_gData.R.................. 19 tests [0;32mOK [0m   test_gData.R.................. 20 tests [0;32mOK [0m 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test_STGHelper.R<117--119>    call| expect_equal(statgenGWAS:::exclMarkers(snpCov = c("SNP1", "SNP2",    call| --> "SNP3"), markers = markers, allFreq = allFreq), c(1, 3, 2))    diff| names for current but not for target   Error: 4 out of 379 tests failed   In addition: Warning message:   In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :     for '← 2@3' in 'mbcsToSbcs': <- substituted for ← (U+2190)   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [89s/115s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 2 NOTEs