• using R Under development (unstable) (2026-03-14 r89623)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-14) 15.2.0     GNU Fortran (Debian 15.2.0-14) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-03-15 14:01:50 UTC
• checking for file ‘asymLD/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘asymLD’ version ‘0.1’
• checking CRAN incoming feasibility ... [1s/2s] NOTE Maintainer: ‘Richard M. Single <rsingle@uvm.edu>’ No Authors@R field in DESCRIPTION. Please add one, modifying   Authors@R: person(given = c("Richard", "M."),                     family = "Single",                     role = c("aut", "cre"),                     email = "rsingle@uvm.edu") as necessary. Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘haplo.stats’
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• checking whether package ‘asymLD’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
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• checking examples ... [0s/0s] ERROR Running examples in ‘asymLD-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compute.ALD > ### Title: Compute ALD. > ### Aliases: compute.ALD > > ### ** Examples > > library(asymLD) > > # An example using haplotype frequencies from Wilson(2010) > data(hla.freqs) > hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",] > compute.ALD(hla.a_b)    ALD.x.y is asymmetric LD for locus x conditioned on locus y   locus1 locus2 F.1 F.1.2 F.2 F.2.1 ALD.1.2 ALD.2.1 1 A B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872 > hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-") > compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])    ALD.x.y is asymmetric LD for locus x conditioned on locus y   locus1 locus2 F.1 F.1.2 F.2 F.2.1 ALD.1.2 ALD.2.1 1 C B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396 > # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but > # ignored by the function. > > # An example using genotype data from the haplo.stats package > require(haplo.stats) Loading required package: haplo.stats Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :   there is no package called ‘haplo.stats’ > data(hla.demo) Warning in data(hla.demo) : data set ‘hla.demo’ not found > geno <- hla.demo[,5:8] #DPB-DPA Error: object 'hla.demo' not found Execution halted
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• DONE

Status: 1 ERROR, 1 NOTE