CRAN Package Check Results for Package qtl

Last updated on 2020-02-24 22:50:34 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.45-11 85.63 302.54 388.17 ERROR
r-devel-linux-x86_64-debian-gcc 1.45-11 59.60 268.20 327.80 OK
r-devel-linux-x86_64-fedora-clang 1.45-11 529.08 NOTE
r-devel-linux-x86_64-fedora-gcc 1.45-11 508.60 OK
r-devel-windows-ix86+x86_64 1.45-11 155.00 463.00 618.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 1.45-11 215.00 634.00 849.00 NOTE
r-patched-linux-x86_64 1.45-11 62.73 327.52 390.25 OK
r-patched-solaris-x86 1.45-11 617.50 NOTE
r-release-linux-x86_64 1.45-11 63.79 329.87 393.66 OK
r-release-windows-ix86+x86_64 1.45-11 154.00 471.00 625.00 NOTE
r-release-osx-x86_64 1.45-11 NOTE
r-oldrel-windows-ix86+x86_64 1.45-11 222.00 443.00 665.00 NOTE
r-oldrel-osx-x86_64 1.45-11 NOTE

Check Details

Version: 1.45-11
Check: examples
Result: ERROR
    Running examples in 'qtl-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: addpair
    > ### Title: Scan for an additional pair of QTL in a multiple-QTL model
    > ### Aliases: addpair
    > ### Keywords: models
    >
    > ### ** Examples
    >
    > # A totally contrived example to show some of what you can do
    >
    > # simulate backcross data with 3 chromosomes (names "17", "18", "19")
    > # one QTL on chr 17 at 40 cM
    > # one QTL on chr 18 at 30 cM
    > # two QTL on chr 19, at 10 and 40 cM
    > data(map10)
    > model <- rbind(c(1,40,0), c(2,30,0), c(3,10,0), c(3,40,0))
    > ## Not run: fakebc <- sim.cross(map10[17:19], model=model, type="bc", n.ind=250)
    > ## Don't show:
    > fakebc <- sim.cross(map10[17:19], model=model, type="bc", n.ind=25)
    > ## End(Don't show)
    >
    > # het at QTL on 17 and 1st QTL on 19 increases phenotype by 1 unit
    > # het at QTL on 18 and 2nd QTL on 19 decreases phenotype by 1 unit
    > qtlgeno <- fakebc$qtlgeno
    > phe <- rnorm(nind(fakebc))
    > w <- qtlgeno[,1]==2 & qtlgeno[,3]==2
    > phe[w] <- phe[w] + 1
    > w <- qtlgeno[,2]==2 & qtlgeno[,4]==2
    > phe[w] <- phe[w] - 1
    > fakebc$pheno[,1] <- phe
    >
    > ## Not run: fakebc <- calc.genoprob(fakebc, step=2, err=0.001)
    > ## Don't show:
    > fakebc <- calc.genoprob(fakebc, step=0, err=0.001)
    > ## End(Don't show)
    >
    > # base model has QTLs on chr 17 and 18
    > qtl <- makeqtl(fakebc, chr=c("17", "18"), pos=c(40,30), what="prob")
    >
    > # scan for an additional pair of QTL, one interacting with the locus
    > # on 17 and one interacting with the locus on 18
    > out.ap <- addpair(fakebc, qtl=qtl, formula = y~Q1*Q3 + Q2*Q4, method="hk")
    Scanning chr 17 and 17
    Scanning chr 17 and 18
    Scanning chr 18 and 17
    Scanning chr 17 and 19
    Scanning chr 19 and 17
    Scanning chr 17 alone
    Scanning chr 18 and 18
    Scanning chr 18 and 19
    Scanning chr 19 and 18
    Scanning chr 18 alone
    Scanning chr 19 and 19
    Scanning chr 19 alone
    >
    > max(out.ap)
    Error in data.frame(chr1 = chr1, chr2 = chr2, pos1.jnt = out$pos1.jnt, :
     arguments imply differing number of rows: 0, 190
    Calls: max.scantwo ... summary.scantwo -> subrousummaryscantwo -> data.frame
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.45-11
Check: tests
Result: ERROR
     Running 'test_io.R' [1s/1s]
     Comparing 'test_io.Rout' to 'test_io.Rout.save' ... OK
     Running 'test_mapqtl_io.R' [5s/5s]
     Comparing 'test_mapqtl_io.Rout' to 'test_mapqtl_io.Rout.save' ... OK
     Running 'test_qtl.R' [6s/7s]
     Running 'test_scanonevar.R' [11s/11s]
     Comparing 'test_scanonevar.Rout' to 'test_scanonevar.Rout.save' ... OK
     Running 'test_tidyIO.R' [1s/1s]
     Comparing 'test_tidyIO.Rout' to 'test_tidyIO.Rout.save' ... OK
     Running 'testaugmentation.R' [3s/3s]
     Running 'testthat.R' [37s/42s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > test_check("qtl")
     Loading required package: qtl
     -- 1. Error: scantwo and scantwopermhk give same results (@test-scantwoperm.R#9)
     invalid 'nrow' value (too large or NA)
     Backtrace:
     1. qtl::scantwo(hyper, method = "hk", n.perm = 3, verbose = FALSE)
     2. qtl:::scantwo.perm(...)
     3. qtl:::scantwo.perm.engine(...)
     5. qtl::subrousummaryscantwo(tem, for.perm = TRUE)
     6. base::matrix(0, nrow = n.chrpair, ncol = n.phe)
    
     -- 2. Error: summary.scantwo works with X-chr-specific perms (@test-scantwoperm.
     invalid 'nrow' value (too large or NA)
     Backtrace:
     1. base::summary(out2, perms = operm1, alpha = 0.05)
     2. qtl:::summary.scantwo(out2, perms = operm1, alpha = 0.05)
     3. qtl::subrousummaryscantwo(object, for.perm = FALSE)
     4. base::matrix(0, nrow = n.chrpair, ncol = n.phe)
    
     == testthat results ===========================================================
     [ OK: 10 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
     1. Error: scantwo and scantwopermhk give same results (@test-scantwoperm.R#9)
     2. Error: summary.scantwo works with X-chr-specific perms (@test-scantwoperm.R#40)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.45-11
Check: installed package size
Result: NOTE
     installed size is 11.5Mb
     sub-directories of 1Mb or more:
     R 1.7Mb
     contrib 3.8Mb
     doc 3.0Mb
     libs 1.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64