CRAN Package Check Results for Package Hmsc

Last updated on 2019-12-10 15:48:02 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.0-2 20.20 152.63 172.83 ERROR
r-devel-linux-x86_64-debian-gcc 3.0-2 18.42 116.17 134.59 ERROR
r-devel-linux-x86_64-fedora-clang 3.0-2 224.20 OK
r-devel-linux-x86_64-fedora-gcc 3.0-2 220.84 OK
r-devel-windows-ix86+x86_64 3.0-2 37.00 167.00 204.00 OK
r-devel-windows-ix86+x86_64-gcc8 3.0-2 39.00 160.00 199.00 OK
r-patched-linux-x86_64 3.0-2 17.42 149.24 166.66 OK
r-patched-solaris-x86 3.0-2 277.30 OK
r-release-linux-x86_64 3.0-2 16.06 148.57 164.63 OK
r-release-windows-ix86+x86_64 3.0-2 37.00 148.00 185.00 OK
r-release-osx-x86_64 3.0-2 OK
r-oldrel-windows-ix86+x86_64 3.0-2 26.00 142.00 168.00 WARN
r-oldrel-osx-x86_64 3.0-2 OK

Check Details

Version: 3.0-2
Check: examples
Result: ERROR
    Running examples in 'Hmsc-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: Hmsc
    > ### Title: Hmsc
    > ### Aliases: Hmsc
    >
    > ### ** Examples
    >
    > # Creating a Hmsc object without phylogeny, trait data or random levels
    > m = Hmsc(Y=TD$Y, XData=TD$X, XFormula=~x1+x2)
    Error in switch(class(hM$X), matrix = { : EXPR must be a length 1 vector
    Calls: Hmsc
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 3.0-2
Check: tests
Result: ERROR
     Running 'testthat.R' [9s/10s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > ## Test `Hmsc` using the `testthat` package
     >
     > ## Setup
     > require("testthat")
     Loading required package: testthat
     > require("Hmsc")
     Loading required package: Hmsc
     Loading required package: coda
     >
     > ## Runs the tests in inst/tests
     > test_check("Hmsc")
     -- 1. Error: WAIC gives correct output (@test-WAIC.R#4) -----------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. testthat::expect_equal(round(computeWAIC(TD$m), 1), 0.8)
     4. Hmsc::computeWAIC(TD$m)
    
     -- 2. Error: computeInitialParameters gives right number of output parameters (@
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 3. Error: Standard initial beta is correct (@test-initialParameters.R#10) --
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 4. Error: Standard initial gamma is correct (@test-initialParameters.R#17) -
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 5. Error: Standard initial V is correct (@test-initialParameters.R#24) -----
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 6. Error: Standard initial Sigma is correct (@test-initialParameters.R#30) -
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 7. Error: Standard initial Eta is distributed as N(0,1) (@test-initialParamet
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 8. Error: Standard initial Alpha is correct (@test-initialParameters.R#46) -
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 9. Error: Standard initial Rho is correct (@test-initialParameters.R#55) ---
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 10. Error: Standard initial Lambda is correct (@test-initialParameters.R#61)
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 11. Error: Standard initial Psi is correct (@test-initialParameters.R#71) --
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 12. Error: Standard initial Delta is correct (@test-initialParameters.R#81)
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 13. Error: Standard initial Z is correct (@test-initialParameters.R#91) ----
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 14. Error: Fixed effects initial beta is correct (@test-initialParameters.R#1
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 15. Error: Fixed effects initial gamma (@test-initialParameters.R#119) -----
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = "fixed effects")
    
     -- 16. Error: Fixed effects initial V (@test-initialParameters.R#130) ---------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = "fixed effects")
    
     -- 17. Error: phylogenetic parameters when phylogeny is not provided (@test-init
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 18. Error: spatial parameters when spatial data is not provided (@test-initia
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 19. Error: updateGamma2 is correct (@test-sampling.R#5) --------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 20. Error: UpdateGammaEta is correct (@test-sampling.R#17) -----------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 21. Error: updateBetaLambda is correct (@test-sampling.R#37) ---------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 22. Error: updateGammaV is correct (@test-sampling.R#55) -------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 23. Error: updateRho is correct (@test-sampling.R#72) ----------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 24. Error: updateLambdaPriors is correct (@test-sampling.R#81) -------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 25. Error: updateEta is correct (@test-sampling.R#98) ----------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     -- 26. Error: updateInvSigma is correct (@test-sampling.R#125) ----------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 27. Error: updateNf is correct (@test-sampling.R#137) ----------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     [1] "Setting updater$Gamma2=FALSE due to specified phylogeny matrix"
     -- 28. Error: sampleMCMC returns m object of right size (@test-sampling.R#166)
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::sampleMcmc(TD$m, samples = 1)
     2. Hmsc:::sampleChain(chain)
     3. Hmsc:::computeInitialParameters(hM, initPar)
    
     -- 29. Failure: Hmsc returns error when XData is not a data frame or list of dat
     `Hmsc(Y = matrix(1:10), XData = matrix(1:10))` threw an error with unexpected message.
     Expected match: "Hmsc.setData: XData must either a data.frame or a list of data.frame objects"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), XData = matrix(1:10))
    
     -- 30. Failure: Hmsc returns error when X or XData contains NA values (@test-set
     `Hmsc(Y = matrix(1:10), X = list(x1 = matrix(c(1:9, NA))))` threw an error with unexpected message.
     Expected match: "all elements of X list must contain no NA values"
     Actual message: "Hmsc.setData: each element of X list must be a matrix"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = list(x1 = matrix(c(1:9, NA))))
    
     -- 31. Failure: Hmsc returns error when X or XData contains NA values (@test-set
     `Hmsc(Y = matrix(1:10), X = matrix(c(1:9, NA)))` threw an error with unexpected message.
     Expected match: "X must contain no NA values"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(c(1:9, NA)))
    
     -- 32. Failure: Hmsc returns error when the size of X or XData is not correct (@
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: for each element of X list the number of rows must be equal to the number of sampling units"
     Actual message: "Hmsc.setData: each element of X list must be a matrix"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 33. Failure: Hmsc returns error when the size of X or XData is not correct (@
     `Hmsc(Y = matrix(1:20, nrow = 10, ncol = 2), X = matrix(1:9))` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in X must be equal to the number of sampling units"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:20, nrow = 10, ncol = 2), X = matrix(1:9))
    
     -- 34. Failure: Hmsc returns error when X contains more than one intercept colum
     `Hmsc(Y = matrix(1:10), X = Xmat)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of X matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = Xmat)
    
     -- 35. Failure: Hmsc returns error when X contains more than one intercept colum
     `Hmsc(Y = matrix(1:10), XData = Xdat)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of X matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), XData = Xdat)
    
     -- 36. Failure: Hmsc returns error when the wrong combination of Tr, TrData and
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: at maximum one of TrData and Tr arguments can be specified"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 37. Failure: Hmsc returns error when the wrong combination of Tr, TrData and
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: TrFormula argument must be specified if TrData is provided"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 38. Failure: Hmsc returns error when the wrong combination of Tr, TrData and
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: Tr must be a matrix"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 39. Failure: Hmsc returns error when trait data does not have the right size
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in Tr should be equal to number of columns in Y"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 40. Failure: Hmsc returns error when trait data does not have the right size
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in TrData should be equal to number of columns in Y"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 41. Failure: Hmsc returns error when there are unknowns in trait data (@test-
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: Tr parameter must not contain any NA values"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 42. Failure: Hmsc returns error when there are unknowns in trait data (@test-
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: TrData parameter must not contain any NA values"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 43. Failure: Hmsc returns error when there are unknowns in trait data (@test-
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "object 't2' not found"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 44. Failure: Hmsc returns error when the intercept columns for Tr is not corr
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of Tr matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 45. Failure: Hmsc returns error when the intercept columns for Tr is not corr
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of Tr matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 46. Failure: Hmsc returns error when the intercept columns for Tr is not corr
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: intercept column in Tr matrix must be a column of ones"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 47. Failure: Hmsc returns error when intercept is specified in TrFormula (@te
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of Tr matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 48. Error: Hmsc returns error when intercept is specified in TrFormula (@test
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 49. Failure: Hmsc returns error when both a tree and a correlation matrix are
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: at maximum one of phyloTree and C arguments can be specified"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 50. Failure: Hmsc returns error when (@test-setHmsc.R#85) -----------------
     `Hmsc(Y = matrix(1:10), X = matrix(1:10), C = TD$C)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the size of square matrix C must be equal to number of species"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10), C = TD$C)
    
     -- 51. Failure: Hmsc returns error when studydesign does not match random levels
     `Hmsc(Y = matrix(1:10), X = matrix(1:10), ranLevels = TD$rL1)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: studyDesign is empty, but ranLevels is not"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10), ranLevels = TD$rL1)
    
     -- 52. Failure: Hmsc returns error when studydesign does not match random levels
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: studyDesign must contain named columns corresponding to all levels listed in ranLevelsUsed"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 53. Failure: Hmsc returns error when studydesign does not match random levels
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: studyDesign must contain named columns corresponding to all levels listed in ranLevelsUsed"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 54. Error: Hmsc returns error when studydesign does not match random levels (
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 55. Failure: Hmsc returns error when studydesign does not match Y (@test-setH
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in studyDesign must be equal to number of rows in Y"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 56. Error: Scaling for Y (@test-setHmsc.R#106) -----------------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(Y = matrix(1:20, nrow = 10, ncol = 2), X = matrix(1:10))
    
     -- 57. Error: Scaling for X (@test-setHmsc.R#122) -----------------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10))
    
     -- 58. Error: Scaling for traits (@test-setHmsc.R#137) ------------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 59. Error: Family set correctly (@test-setHmsc.R#151) ----------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 60. Error: Variance set correctly (@test-setHmsc.R#155) --------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 61. Failure: Hmsc returns error when unsuitable data model is given (@test-se
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: some of the distributions ill defined"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     -- 62. Error: Hmsc is set correctly (@test-setHmsc.R#167) ---------------------
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     -- 63. Error: Hmsc returns error when phylo prior is incorrect (@test-setPriors.
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10))
    
     == testthat results ===========================================================
     [ OK: 56 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 63 ]
     1. Error: WAIC gives correct output (@test-WAIC.R#4)
     2. Error: computeInitialParameters gives right number of output parameters (@test-initialParameters.R#4)
     3. Error: Standard initial beta is correct (@test-initialParameters.R#10)
     4. Error: Standard initial gamma is correct (@test-initialParameters.R#17)
     5. Error: Standard initial V is correct (@test-initialParameters.R#24)
     6. Error: Standard initial Sigma is correct (@test-initialParameters.R#30)
     7. Error: Standard initial Eta is distributed as N(0,1) (@test-initialParameters.R#35)
     8. Error: Standard initial Alpha is correct (@test-initialParameters.R#46)
     9. Error: Standard initial Rho is correct (@test-initialParameters.R#55)
     1. ...
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 3.0-2
Check: tests
Result: ERROR
     Running ‘testthat.R’ [6s/11s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > ## Test `Hmsc` using the `testthat` package
     >
     > ## Setup
     > require("testthat")
     Loading required package: testthat
     > require("Hmsc")
     Loading required package: Hmsc
     Loading required package: coda
     >
     > ## Runs the tests in inst/tests
     > test_check("Hmsc")
     ── 1. Error: WAIC gives correct output (@test-WAIC.R#4) ───────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. testthat::expect_equal(round(computeWAIC(TD$m), 1), 0.8)
     4. Hmsc::computeWAIC(TD$m)
    
     ── 2. Error: computeInitialParameters gives right number of output parameters (@
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 3. Error: Standard initial beta is correct (@test-initialParameters.R#10) ──
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 4. Error: Standard initial gamma is correct (@test-initialParameters.R#17) ─
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 5. Error: Standard initial V is correct (@test-initialParameters.R#24) ─────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 6. Error: Standard initial Sigma is correct (@test-initialParameters.R#30) ─
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 7. Error: Standard initial Eta is distributed as N(0,1) (@test-initialParamet
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 8. Error: Standard initial Alpha is correct (@test-initialParameters.R#46) ─
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 9. Error: Standard initial Rho is correct (@test-initialParameters.R#55) ───
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 10. Error: Standard initial Lambda is correct (@test-initialParameters.R#61)
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 11. Error: Standard initial Psi is correct (@test-initialParameters.R#71) ──
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 12. Error: Standard initial Delta is correct (@test-initialParameters.R#81)
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 13. Error: Standard initial Z is correct (@test-initialParameters.R#91) ────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 14. Error: Fixed effects initial beta is correct (@test-initialParameters.R#1
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 15. Error: Fixed effects initial gamma (@test-initialParameters.R#119) ─────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = "fixed effects")
    
     ── 16. Error: Fixed effects initial V (@test-initialParameters.R#130) ─────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = "fixed effects")
    
     ── 17. Error: phylogenetic parameters when phylogeny is not provided (@test-init
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 18. Error: spatial parameters when spatial data is not provided (@test-initia
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 19. Error: updateGamma2 is correct (@test-sampling.R#5) ────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 20. Error: UpdateGammaEta is correct (@test-sampling.R#17) ─────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 21. Error: updateBetaLambda is correct (@test-sampling.R#37) ───────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 22. Error: updateGammaV is correct (@test-sampling.R#55) ───────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 23. Error: updateRho is correct (@test-sampling.R#72) ──────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 24. Error: updateLambdaPriors is correct (@test-sampling.R#81) ─────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 25. Error: updateEta is correct (@test-sampling.R#98) ──────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc:::computeInitialParameters(TD$m, initPar = NULL)
    
     ── 26. Error: updateInvSigma is correct (@test-sampling.R#125) ────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 27. Error: updateNf is correct (@test-sampling.R#137) ──────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     [1] "Setting updater$Gamma2=FALSE due to specified phylogeny matrix"
     ── 28. Error: sampleMCMC returns m object of right size (@test-sampling.R#166)
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::sampleMcmc(TD$m, samples = 1)
     2. Hmsc:::sampleChain(chain)
     3. Hmsc:::computeInitialParameters(hM, initPar)
    
     ── 29. Failure: Hmsc returns error when XData is not a data frame or list of dat
     `Hmsc(Y = matrix(1:10), XData = matrix(1:10))` threw an error with unexpected message.
     Expected match: "Hmsc.setData: XData must either a data.frame or a list of data.frame objects"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), XData = matrix(1:10))
    
     ── 30. Failure: Hmsc returns error when X or XData contains NA values (@test-set
     `Hmsc(Y = matrix(1:10), X = list(x1 = matrix(c(1:9, NA))))` threw an error with unexpected message.
     Expected match: "all elements of X list must contain no NA values"
     Actual message: "Hmsc.setData: each element of X list must be a matrix"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = list(x1 = matrix(c(1:9, NA))))
    
     ── 31. Failure: Hmsc returns error when X or XData contains NA values (@test-set
     `Hmsc(Y = matrix(1:10), X = matrix(c(1:9, NA)))` threw an error with unexpected message.
     Expected match: "X must contain no NA values"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(c(1:9, NA)))
    
     ── 32. Failure: Hmsc returns error when the size of X or XData is not correct (@
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: for each element of X list the number of rows must be equal to the number of sampling units"
     Actual message: "Hmsc.setData: each element of X list must be a matrix"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 33. Failure: Hmsc returns error when the size of X or XData is not correct (@
     `Hmsc(Y = matrix(1:20, nrow = 10, ncol = 2), X = matrix(1:9))` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in X must be equal to the number of sampling units"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:20, nrow = 10, ncol = 2), X = matrix(1:9))
    
     ── 34. Failure: Hmsc returns error when X contains more than one intercept colum
     `Hmsc(Y = matrix(1:10), X = Xmat)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of X matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = Xmat)
    
     ── 35. Failure: Hmsc returns error when X contains more than one intercept colum
     `Hmsc(Y = matrix(1:10), XData = Xdat)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of X matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), XData = Xdat)
    
     ── 36. Failure: Hmsc returns error when the wrong combination of Tr, TrData and
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: at maximum one of TrData and Tr arguments can be specified"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 37. Failure: Hmsc returns error when the wrong combination of Tr, TrData and
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: TrFormula argument must be specified if TrData is provided"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 38. Failure: Hmsc returns error when the wrong combination of Tr, TrData and
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: Tr must be a matrix"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 39. Failure: Hmsc returns error when trait data does not have the right size
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in Tr should be equal to number of columns in Y"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 40. Failure: Hmsc returns error when trait data does not have the right size
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in TrData should be equal to number of columns in Y"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 41. Failure: Hmsc returns error when there are unknowns in trait data (@test-
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: Tr parameter must not contain any NA values"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 42. Failure: Hmsc returns error when there are unknowns in trait data (@test-
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: TrData parameter must not contain any NA values"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 43. Failure: Hmsc returns error when there are unknowns in trait data (@test-
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "object 't2' not found"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 44. Failure: Hmsc returns error when the intercept columns for Tr is not corr
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of Tr matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 45. Failure: Hmsc returns error when the intercept columns for Tr is not corr
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of Tr matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 46. Failure: Hmsc returns error when the intercept columns for Tr is not corr
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: intercept column in Tr matrix must be a column of ones"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 47. Failure: Hmsc returns error when intercept is specified in TrFormula (@te
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: only one column of Tr matrix could be named Intercept or (Intercept)"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 48. Error: Hmsc returns error when intercept is specified in TrFormula (@test
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 49. Failure: Hmsc returns error when both a tree and a correlation matrix are
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: at maximum one of phyloTree and C arguments can be specified"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 50. Failure: Hmsc returns error when (@test-setHmsc.R#85) ─────────────────
     `Hmsc(Y = matrix(1:10), X = matrix(1:10), C = TD$C)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the size of square matrix C must be equal to number of species"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10), C = TD$C)
    
     ── 51. Failure: Hmsc returns error when studydesign does not match random levels
     `Hmsc(Y = matrix(1:10), X = matrix(1:10), ranLevels = TD$rL1)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: studyDesign is empty, but ranLevels is not"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10), ranLevels = TD$rL1)
    
     ── 52. Failure: Hmsc returns error when studydesign does not match random levels
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: studyDesign must contain named columns corresponding to all levels listed in ranLevelsUsed"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 53. Failure: Hmsc returns error when studydesign does not match random levels
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: studyDesign must contain named columns corresponding to all levels listed in ranLevelsUsed"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 54. Error: Hmsc returns error when studydesign does not match random levels (
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 55. Failure: Hmsc returns error when studydesign does not match Y (@test-setH
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: the number of rows in studyDesign must be equal to number of rows in Y"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 56. Error: Scaling for Y (@test-setHmsc.R#106) ─────────────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(Y = matrix(1:20, nrow = 10, ncol = 2), X = matrix(1:10))
    
     ── 57. Error: Scaling for X (@test-setHmsc.R#122) ─────────────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10))
    
     ── 58. Error: Scaling for traits (@test-setHmsc.R#137) ────────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 59. Error: Family set correctly (@test-setHmsc.R#151) ──────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 60. Error: Variance set correctly (@test-setHmsc.R#155) ────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 61. Failure: Hmsc returns error when unsuitable data model is given (@test-se
     `Hmsc(...)` threw an error with unexpected message.
     Expected match: "Hmsc.setData: some of the distributions ill defined"
     Actual message: "EXPR must be a length 1 vector"
     Backtrace:
     1. testthat::expect_error(...)
     6. Hmsc::Hmsc(...)
    
     ── 62. Error: Hmsc is set correctly (@test-setHmsc.R#167) ─────────────────────
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(...)
    
     ── 63. Error: Hmsc returns error when phylo prior is incorrect (@test-setPriors.
     EXPR must be a length 1 vector
     Backtrace:
     1. Hmsc::Hmsc(Y = matrix(1:10), X = matrix(1:10))
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 56 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 63 ]
     1. Error: WAIC gives correct output (@test-WAIC.R#4)
     2. Error: computeInitialParameters gives right number of output parameters (@test-initialParameters.R#4)
     3. Error: Standard initial beta is correct (@test-initialParameters.R#10)
     4. Error: Standard initial gamma is correct (@test-initialParameters.R#17)
     5. Error: Standard initial V is correct (@test-initialParameters.R#24)
     6. Error: Standard initial Sigma is correct (@test-initialParameters.R#30)
     7. Error: Standard initial Eta is distributed as N(0,1) (@test-initialParameters.R#35)
     8. Error: Standard initial Alpha is correct (@test-initialParameters.R#46)
     9. Error: Standard initial Rho is correct (@test-initialParameters.R#55)
     1. ...
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 3.0-2
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
Flavor: r-oldrel-windows-ix86+x86_64