* using log directory ‘/Users/ripley/R/packages/tests-devel/nadiv.Rcheck’ * using R Under development (unstable) (2023-11-28 r85645) * using platform: aarch64-apple-darwin23.1.0 * R was compiled by Apple clang version 15.0.0 (clang-1500.1.0.2.5) GNU Fortran (GCC) 12.2.0 * running under: macOS Sonoma 14.1.1 * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘nadiv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘nadiv’ version ‘2.17.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘asreml’ * 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 ‘nadiv’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX14.2.sdk’ * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... ERROR Running examples in ‘nadiv-Ex.R’ failed The error most likely occurred in: > ### Name: makeAinv > ### Title: Creates the inverse additive genetic relationship matrix > ### Aliases: makeAinv makeAinv.default makeAinv.fuzzy makeGGAinv > > ### ** Examples > > > ## Without genetic groups ## > makeAinv(Mrode2) $Ainv 6 x 6 sparse Matrix of class "dgCMatrix" 1 1.8333333 0.5000000 -1.0 -0.6666667 . . 2 0.5000000 2.0333333 -1.0 . 0.5333333 -1.066667 3 -1.0000000 -1.0000000 2.5 0.5000000 -1.0000000 . 4 -0.6666667 . 0.5 1.8333333 -1.0000000 . 5 . 0.5333333 -1.0 -1.0000000 2.5333333 -1.066667 6 . -1.0666667 . . -1.0666667 2.133333 $listAinv row column Ainv 1 1 1 1.8333333 5 2 1 0.5000000 6 2 2 2.0333333 10 3 1 -1.0000000 11 3 2 -1.0000000 12 3 3 2.5000000 15 4 1 -0.6666667 16 4 3 0.5000000 17 4 4 1.8333333 19 5 2 0.5333333 20 5 3 -1.0000000 21 5 4 -1.0000000 22 5 5 2.5333333 24 6 2 -1.0666667 25 6 5 -1.0666667 26 6 6 2.1333333 $f [1] 0.000 0.000 0.000 0.000 0.125 0.125 $logDet [1] -2.431662 $dii [1] 1.00000 1.00000 0.50000 0.75000 0.50000 0.46875 > > ## With genetic groups ## > ## Type A > typeAped <- Q1988[-c(3:7), c("id", "damGG", "sireGG")] > AstarA <- makeAinv(typeAped, ggroups = 2, gOnTop = FALSE)$Ainv > ## Type D > typeDped <- Q1988[-c(1:7), c("id", "damGG", "sireGG")] > AstarD <- makeAinv(typeDped, ggroups = c("g1", "g2"), gOnTop = FALSE)$Ainv > stopifnot(identical(AstarA, AstarD)) > > # Show that the augmented A-inverse with genetic groups > # contains the normal A-inverse (i.e., without genetic groups) > ## Augmented A-inverse with genetic groups > ggAinv <- makeAinv(Mrode3[-c(1,2), c("calf", "damGG", "sireGG")], + ggroups = c("g1", "g2"), gOnTop = FALSE)$Ainv > noggAinv <- makeAinv(Mrode3[-c(1,2), c("calf", "dam", "sire")], + ggroups = NULL)$Ainv > # First 8 rows & columns of ggAinv are same as A-inverse without > ## genetic groups > ggAinv[1:8, 1:8] 8 x 8 sparse Matrix of class "dgCMatrix" 1 1.8333333 0.5 . -0.6666667 . -1.0 . . 2 0.5000000 2.0 0.5 . -1.0 -1.0 . . 3 . 0.5 2.0 . -1.0 0.5 . -1 4 -0.6666667 . . 1.8333333 0.5 . -1 . 5 . -1.0 -1.0 0.5000000 2.5 . -1 . 6 -1.0000000 -1.0 0.5 . . 2.5 . -1 7 . . . -1.0000000 -1.0 . 2 . 8 . . -1.0 . . -1.0 . 2 > noggAinv 8 x 8 sparse Matrix of class "dgCMatrix" 1 1.8333333 0.5 . -0.6666667 . -1.0 . . 2 0.5000000 2.0 0.5 . -1.0 -1.0 . . 3 . 0.5 2.0 . -1.0 0.5 . -1 4 -0.6666667 . . 1.8333333 0.5 . -1 . 5 . -1.0 -1.0 0.5000000 2.5 . -1 . 6 -1.0000000 -1.0 0.5 . . 2.5 . -1 7 . . . -1.0000000 -1.0 . 2 . 8 . . -1.0 . . -1.0 . 2 > stopifnot(all.equal(ggAinv[1:8, 1:8], noggAinv)) Error: ggAinv[1:8, 1:8] and noggAinv are not equal: Attributes: < Modes: NULL, list > Attributes: < Lengths: 0, 1 > Attributes: < names for current but not for target > .... Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/Users/ripley/R/packages/tests-devel/nadiv.Rcheck/00check.log’ for details. 33.43 real 28.07 user 4.37 sys