R Under development (unstable) (2024-09-23 r87189 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## follow http://adv-r.had.co.nz/Testing.html > print(sprintf("Test seqminer [version %s]", packageVersion("seqminer"))) [1] "Test seqminer [version 9.5]" > print("Platform") [1] "Platform" > print(str(.Platform)) List of 8 $ OS.type : chr "windows" $ file.sep : chr "/" $ dynlib.ext: chr ".dll" $ GUI : chr "RTerm" $ endian : chr "little" $ pkgType : chr "win.binary" $ path.sep : chr ";" $ r_arch : chr "x64" NULL > > print("Sys.info()") [1] "Sys.info()" > print(Sys.info()) sysname release version nodename machine "Windows" "Server x64" "build 20348" "CRANWIN3" "x86-64" login user effective_user udomain "CRAN" "CRAN" "CRAN" "CRANWIN3" > > print(citation("seqminer")) To cite package 'seqminer' in publications use: Zhan X, Liu D (2015). "SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations." _Genetic Epidemiology_, *39*(8), 1242. doi:10.1002/gepi.21918 , seqminer version 9.5, . A BibTeX entry for LaTeX users is @Article{, title = {SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations}, author = {Xiaowei Zhan and Dajiang J Liu}, journal = {Genetic Epidemiology}, volume = {39}, number = {8}, pages = {1242}, year = {2015}, note = {seqminer version 9.5}, web = {http:/zhanxw.github.io/seqminer}, publisher = {Wiley Online Library}, url = {http://dx.doi.org/10.1002/gepi.21918}, doi = {10.1002/gepi.21918}, } > > library(testthat) > library(seqminer) > ## ## test code are under inst/tests > ## ## test_package("seqminer", reporter="tap") > ## test_package("seqminer") > test_check("seqminer") 1 gene/region to be extracted. Read score tests... In study 0 Done read score file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/bi.MetaScore.assoc.gz Read cov files ... In study 0 Done read cov file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/bi.MetaCov.assoc.gz Finished calculation. [1] "1:1" "1:2" "1:3" [[1]] [1] "G" "G" "G" [[1]] [,1] [,2] [,3] [1,] 0.5126420 -0.0427202 0.0427202 [2,] -0.0427202 0.1993610 -0.0284801 [3,] 0.0427202 -0.0284801 0.1139210 Skipped: encounter a duplicated site: [ 1:1 ] in file [ D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/tri.MetaScore.assoc.gz ] 1 gene/region to be extracted. Read score tests... In study 0 Error: encounter a duplicated location: [ 1:1 ] in file [ D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results! Done read score file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/tri.MetaScore.assoc.gz Read cov files ... In study 0 Done read cov file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/tri.MetaCov.assoc.gz Finished calculation. [1] "1:1" "1:3" [[1]] [1] "T" "G" [[1]] [,1] [,2] [1,] 0.1993610 -0.0284801 [2,] -0.0284801 0.1139210 1 gene/region to be extracted. Read score tests... In study 0 Done read score file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/tri.MetaScore.assoc.gz Read cov files ... In study 0 Done read cov file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/tri.MetaCov.assoc.gz Finished calculation. [1] "1:1_A/G" "1:1_A/T" "1:3_A/G" [[1]] [1] "G" "T" "G" [[1]] [,1] [,2] [,3] [1,] 0.5126420 -0.0427202 0.0427202 [2,] -0.0427202 0.1993610 -0.0284801 [3,] 0.0427202 -0.0284801 0.1139210 [1] "=============" Total 3 line loaded, now put them to matrix [ 3 x 3 ] in R ... 1:1 1:2 1:3 1:1 0.5126420 -0.0427202 0.0427202 1:2 -0.0427202 0.1993610 -0.0284801 1:3 0.0427202 -0.0284801 0.1139210 1:1 1:2 1:3 1:1 0.5126420 -0.0427202 0.0427202 1:2 -0.0427202 0.1993610 -0.0284801 1:3 0.0427202 -0.0284801 0.1139210 Total 3 line loaded, now put them to matrix [ 3 x 3 ] in R ... 1:1 1:1/1 1:3 1:1 0.5126420 -0.0427202 0.0427202 1:1/1 -0.0427202 0.1993610 -0.0284801 1:3 0.0427202 -0.0284801 0.1139210 [1] "=============" $pos [1] 1 2 3 $ref [1] "A" "A" "A" $alt [1] "G" "G" "G" $nSample [1] 9 9 9 $af [1] 0.3333330 0.1111110 0.0555556 $ac [1] 6 2 1 $callRate [1] 1 1 1 $hwe [1] "1" "1" "1" $nref [1] 4 7 8 $nhet [1] 4 2 1 $nalt [1] 1 0 0 $ustat [1] 0.283603 0.000000 0.325521 $vstat [1] 2.14797 1.33950 1.01256 $effect [1] 0.0614687 0.0000000 0.3174930 $pVal [1] 0.894958 1.000000 0.747845 $anno [1] "" "" "" $annoFull [1] "" "" "" $pos [1] 1 1 3 $ref [1] "A" "A" "A" $alt [1] "G" "T" "G" $nSample [1] 9 9 9 $af [1] 0.3333330 0.1111110 0.0555556 $ac [1] 6 2 1 $callRate [1] 1 1 1 $hwe [1] "1" "1" "1" $nref [1] 4 7 8 $nhet [1] 4 2 1 $nalt [1] 1 0 0 $ustat [1] 0.283603 0.000000 0.325521 $vstat [1] 2.14797 1.33950 1.01256 $effect [1] 0.0614687 0.0000000 0.3174930 $pVal [1] 0.894958 1.000000 0.747845 $anno [1] "" "" "" $annoFull [1] "" "" "" Skipped: encounter a duplicated site: [ 1:1 ] in file [ D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ] 1 gene/region to be extracted. Read score tests... In study 0 Error: encounter a duplicated location: [ 1:1 ] in file [ D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results! Done read score file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz In study 1 Done read score file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz Read cov files ... In study 0 Done read cov file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz In study 1 Done read cov file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study2.MetaCov.assoc.gz Finished calculation. 1 gene/region to be extracted. Read score tests... In study 0 Done read score file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz In study 1 Done read score file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz Read cov files ... In study 0 Done read cov file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz In study 1 Done read cov file: D:/RCompile/CRANincoming/R-devel/lib/seqminer/test-triallelic/test2.study2.MetaCov.assoc.gz Finished calculation. Loading objects: apoe cfh cfh.all cfh.nonsyn cfh.nonsyn.2 cfh.range cfh.syn cfh.syn.2 out.gene.1 out.gene.2 out.gene.3 out.range.1 ssss --------------- test readVCFToMatrixByRange --------------- 1 region to be extracted. 1 region to be extracted. 2 region to be extracted. 1 region to be extracted. 1 region to be extracted. range of [ CFH ] is [ 1:196621007-196716634 ] 1 region to be extracted. range of [ APOE ] is [ 19:45409038-45412650 ] 1 region to be extracted. range of [ ssss ] is [ ] range of [ CFH ] is [ 1:196621007-196716634 ] range = 1:196621007-196716634 range of [ CFH ] is [ 1:196621007-196716634 ] range = 1:196621007-196716634 range of [ CFH ] is [ 1:196621007-196716634 ] range = 1:196621007-196716634 1 region to be extracted. 1 region to be extracted. 1 region to be extracted. range of [ CFH ] is [ 1:196621007-196716634 ] range of [ CFH ] is [ 1:196621007-196716634 ] range = 1:196621007-196716634 start file = D:/RCompile/CRANincoming/R-devel/lib/seqminer/plink/all.anno.filtered.extract Wed Sep 25 18:52:04 2024 - read bim Wed Sep 25 18:52:04 2024 - read fam extract 2 marker and 3 sample out of 166 marker and 3 sample Wed Sep 25 18:52:04 2024 - read bed Binary PLINK BED file is ready to read build a look-up table assigned 6 values allocate dim and dimnames Wed Sep 25 18:52:04 2024 - end --------------- test openPlink --------------- --------------- test readPlinkBySubscript --------------- start file = D:/RCompile/CRANincoming/R-devel/lib/seqminer/plink/all.anno.filtered.extract.bed extract 2 marker and 3 sample out of 166 marker and 3 sample Binary PLINK BED file is ready to read build a look-up table assigned 6 values allocate dim Wed Sep 25 18:52:04 2024 - end --------------- test readSingleChromosomeVCFToMatrixByRange --------------- fsize = 2688 query [0, 0] Found 1 results found 1 position, e.g. 0 0 Inferred 3 samples from header 1 region to be extracted. query [196621007, 196716634] Found 166 results found 166 position, e.g. -771751936 0 --------------- test createSingleChromosomeVCFIndex --------------- header line has 3 samples offset = 2384 Indexing finished with 3 samples and 166 markers created index file [ D:\temp\Rtmp6PZUFd\file2b141a3853b8 ] --------------- test readSingleChromosomeBCFToMatrixByRange --------------- fsize = 2688 l_text = 4206 Total contig parse = 1, total header index used = 47 Inferred 3 samples from header 1 region to be extracted. query [196621006, 196716633] Found 166 results 1.96623e+08 4215 found 166 position, e.g. 1.96623e+08 4215 sampleNames.size() = 3, markerNames.size() = 166 --------------- test createSingleChromosomeBCFIndex --------------- l_text = 4206 Total contig parse = 1, total header index used = 47 offset_header = 4135 sample size = 3 last character is s[after_chrom_size-1] = 0 Indexing finished with 3 samples and 166 markers created index file [ D:\temp\Rtmp6PZUFd\file2b14376641b5 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 74 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 74 ] > > proc.time() user system elapsed 1.01 0.17 1.64