Fix poppr for upcoming release of adegenet/pegas/hierfstat about poppr HOT 6 CLOSED

Amova tests : 12
Graph color conversion tests : 3
Population Distance Tests : 45
Errors and Exceptions : ...
Genclone coercion tests : 67
Greyscale tests : ...
Data import tests : 89
Missing tests : ....a
Multilocus genotype tests : ...bcdef
Polyploid Tests : .gh.
Poppr table tests : ij
Population subset tests : .................kl
Analytical value tests : .....m...


1. Error: Amova returns published values --------------------------------------------------
invalid class “genind” object: slots in class definition but not in object: "strata", "hierarchy"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: poppr.amova(Aeut, ~Pop/Subpop, quiet = TRUE) at test-amova.R:5
5: is.genind(x) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/amova.r:203
6: validObject(x)
7: stop(msg, ": ", errors, domain = NA)

2. Error: AMOVA handles subsetted genclone objects ----------------------------------------
no slot of name "strata" for this object of class "genind"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: as.genclone(Aeut) at test-amova.R:26
5: as.genclone(Aeut)
6: new("genclone", x) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:555
7: initialize(value, ...)
8: initialize(value, ...)
9: .local(.Object, ...)
10: lapply(names(gen), function(y) slot(.Object, y) <<- slot(gen, y)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407
11: FUN(c("strata", "hierarchy", "tab", "loc.names", "loc.fac", "loc.nall", "all.names", "call", 
   "ind.names", "pop", "pop.names", "ploidy", "type", "other")[[1L]], ...)
12: slot(gen, y) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407

3. Error: graph colors are correctly converted --------------------------------------------
no slot of name "strata" for this object of class "genind"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: partial_clone[1:11] at test-colors.R:6
5: partial_clone[1:11]
6: .local(x, i, j, ..., drop = drop)

4. Error: dist.genpop matches distance ----------------------------------------------------
$ operator is invalid for atomic vectors
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: as.vector(nei.dist(nanpop)) at test-distpop.R:6
5: nei.dist(nanpop)
6: get_gen_mat(x) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/distances.r:222

5. Error: aboot works with diss.dist ------------------------------------------------------
REAL() can only be applied to a 'numeric', not a 'integer'
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: aboot(nan1, dist = diss.dist, sample = 2, quiet = TRUE, showtree = FALSE) at test-distpop.R:21
5: treefunk(xboot) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/distances.r:495
6: TREEFUNK(do.call(DISTFUNK, distargs)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/internal.r:1585
7: as.dist(D)
8: do.call(DISTFUNK, distargs)
9: (function (x, percent = FALSE, mat = FALSE) 
   {
       stopifnot(is(x, "gen"))
       ploid <- x@ploidy
       if (is(x, "bootgen")) {
           ind.names <- x@names
       }
       else {
           ind.names <- x@ind.names
       }
       inds <- nrow(x@tab)
       np <- choose(inds, 2)
       dist.mat <- matrix(data = 0, nrow = inds, ncol = inds)
       numLoci <- length(x@loc.names)
       type <- x@type
       if (type == "PA") {
           dist_by_locus <- matrix(.Call("pairdiffs", x@tab))
           ploid <- 1
       }
       else if (is(x, "bootgen")) {
           dist_by_locus <- vapply(1:numLoci, function(i) {
               .Call("pairdiffs", get_gen_mat(x[, i])) * (ploid/2)
           }, numeric(np))
       }
       else {
           x <- seploc(x)
           dist_by_locus <- vapply(x, function(x) .Call("pairdiffs", x@tab) * (ploid/2), numeric(np))
       }
       dist.mat[lower.tri(dist.mat)] <- rowSums(dist_by_locus)
       colnames(dist.mat) <- ind.names
       rownames(dist.mat) <- ind.names
       if (percent) {
           dist.mat <- dist.mat/(numLoci * ploid)
       }
       dist.mat <- as.dist(dist.mat)
       if (mat == TRUE) {
           dist.mat <- as.matrix(dist.mat)
       }
       return(dist.mat)
   })(x = <S4 object of class structure("bootgen", package = "poppr")>, percent = FALSE, mat = FALSE)
10: vapply(1:numLoci, function(i) {
       .Call("pairdiffs", get_gen_mat(x[, i])) * (ploid/2)
   }, numeric(np)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/distances.r:104
11: FUN(1:9[[1L]], ...)

6. Error: A genclone object contains a genind object --------------------------------------
no slot of name "strata" for this object of class "genind"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: as.genclone(partial_clone) at test-genclone.R:6
5: as.genclone(partial_clone)
6: new("genclone", x) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:555
7: initialize(value, ...)
8: initialize(value, ...)
9: .local(.Object, ...)
10: lapply(names(gen), function(y) slot(.Object, y) <<- slot(gen, y)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407
11: FUN(c("strata", "hierarchy", "tab", "loc.names", "loc.fac", "loc.nall", "all.names", "call", 
   "ind.names", "pop", "pop.names", "ploidy", "type", "other")[[1L]], ...)
12: slot(gen, y) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407

7. Error: Hierarchy methods work for genclone objects. ------------------------------------
no slot of name "strata" for this object of class "genind"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: as.genclone(Aeut) at test-genclone.R:23
5: as.genclone(Aeut)
6: new("genclone", x) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:555
7: initialize(value, ...)
8: initialize(value, ...)
9: .local(.Object, ...)
10: lapply(names(gen), function(y) slot(.Object, y) <<- slot(gen, y)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407
11: FUN(c("strata", "hierarchy", "tab", "loc.names", "loc.fac", "loc.nall", "all.names", "call", 
   "ind.names", "pop", "pop.names", "ploidy", "type", "other")[[1L]], ...)
12: slot(gen, y) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407

8. Error: basic text connections work -----------------------------------------------------
no slot of name "strata" for this object of class "genclone"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_equal(gen@tab, monpop[1:6, drop = TRUE]@tab) at test-import.R:16
5: expect_that(object, equals(expected, label = expected.label, ...), info = info, label = label)
6: condition(object)
7: compare(expected, actual, ...)
8: monpop[1:6, drop = TRUE]
9: monpop[1:6, drop = TRUE]
10: callNextMethod() at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:297
11: .nextMethod(x = x, i = i, drop = drop, ...)
12: .local(x, i, j, ..., drop = drop)

9. Error: genclone objects can be saved and restored --------------------------------------
argument "tab" is missing, with no default
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: genind2genalex(monpop, filename = mp, quiet = TRUE) at test-import.R:21
5: is.genind(pop) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/file_handling.r:438
6: validObject(x)
7: anyStrings(validityMethod(as(object, superClass)))
8: validityMethod(as(object, superClass))
9: ncol(object@tab)
10: as(object, superClass)
11: asMethod(object)
12: new(structure("genind", package = "adegenet"))
13: initialize(value, ...)
14: initialize(value, ...)
15: .local(.Object, ...)
16: colnames(tab)
17: is.data.frame(x)

a. Error: missingno matches na.replace ----------------------------------------------------
could not find function "na.replace"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_identical(missingno(nancycats, "zero", quiet = TRUE), na.replace(nancycats, "0", quiet = TRUE)) at test-missing.R:16
5: expect_that(object, is_identical_to(expected, label = expected.label), info = info, label = label)
6: condition(object)
7: identical(actual, expected)
8: missingno(nancycats, "zero", quiet = TRUE)

b. Error: multilocus genotype vector is same length as samples ----------------------------
invalid class “genind” object: slots in class definition but not in object: "strata", "hierarchy"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_that(length(unique(amlg)), equals(mlg(Aeut, quiet = TRUE))) at test-mlg.R:13
5: condition(object)
6: compare(expected, actual, ...)
7: mlg(Aeut, quiet = TRUE)
8: is.genind(pop) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/mlg.r:180
9: validObject(x)
10: stop(msg, ": ", errors, domain = NA)

c. Error: multilocus genotype matrix matches mlg.vector and data --------------------------
no slot of name "strata" for this object of class "genind"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: as.genclone(Aeut) at test-mlg.R:22
5: as.genclone(Aeut)
6: new("genclone", x) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:555
7: initialize(value, ...)
8: initialize(value, ...)
9: .local(.Object, ...)
10: lapply(names(gen), function(y) slot(.Object, y) <<- slot(gen, y)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407
11: FUN(c("strata", "hierarchy", "tab", "loc.names", "loc.fac", "loc.nall", "all.names", "call", 
   "ind.names", "pop", "pop.names", "ploidy", "type", "other")[[1L]], ...)
12: slot(gen, y) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407

d. Error: mlg.crosspop will work with subsetted genclone objects --------------------------
no slot of name "strata" for this object of class "genind"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: as.genclone(Aeut) at test-mlg.R:39
5: as.genclone(Aeut)
6: new("genclone", x) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:555
7: initialize(value, ...)
8: initialize(value, ...)
9: .local(.Object, ...)
10: lapply(names(gen), function(y) slot(.Object, y) <<- slot(gen, y)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407
11: FUN(c("strata", "hierarchy", "tab", "loc.names", "loc.fac", "loc.nall", "all.names", "call", 
   "ind.names", "pop", "pop.names", "ploidy", "type", "other")[[1L]], ...)
12: slot(gen, y) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/methods.r:407

e. Error: mlg.id Aeut works ---------------------------------------------------------------
invalid class “genind” object: slots in class definition but not in object: "strata", "hierarchy"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: mlg.id(Aeut) at test-mlg.R:103
5: is.genind(pop) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/mlg.r:405
6: validObject(x)
7: stop(msg, ": ", errors, domain = NA)

f. Error: mlg.id Pinf works ---------------------------------------------------------------
argument "tab" is missing, with no default
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: mlg.id(Pinf) at test-mlg.R:142
5: is.genind(pop) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/mlg.r:405
6: validObject(x)
7: anyStrings(validityMethod(as(object, superClass)))
8: validityMethod(as(object, superClass))
9: ncol(object@tab)
10: as(object, superClass)
11: asMethod(object)
12: new(structure("genind", package = "adegenet"))
13: initialize(value, ...)
14: initialize(value, ...)
15: .local(.Object, ...)
16: colnames(tab)
17: is.data.frame(x)

g. Failure(@test-polyploids.R#8): recode_polyploids works as expected ---------------------
testgid@tab[2, -1] not equal to expected
Mean absolute difference: 1

h. Failure(@test-polyploids.R#9): recode_polyploids works as expected ---------------------
testrec@tab[1, ] not equal to expected
Mean relative difference: 1

i. Error: poppr returns expected PA values ------------------------------------------------
invalid class “genind” object: slots in class definition but not in object: "strata", "hierarchy"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: poppr(Aeut, quiet = TRUE) at test-poppr.R:5
5: process_file(dat, missing = missing, cutoff = cutoff, clonecorrect = clonecorrect, hier = hier, 
       dfname = dfname, keep = keep, quiet = TRUE) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/Index_calculations.r:222
6: is.genind(input) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/internal.r:181
7: validObject(x)
8: stop(msg, ": ", errors, domain = NA)

j. Error: poppr returns expected codominant values ----------------------------------------
invalid class “genind” object: slots in class definition but not in object: "strata", "hierarchy"
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: poppr(partial_clone, quiet = TRUE) at test-poppr.R:39
5: process_file(dat, missing = missing, cutoff = cutoff, clonecorrect = clonecorrect, hier = hier, 
       dfname = dfname, keep = keep, quiet = TRUE) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/Index_calculations.r:222
6: is.genind(input) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/internal.r:181
7: validObject(x)
8: stop(msg, ": ", errors, domain = NA)

k. Error: subsetting doesn't work without populations -------------------------------------
error in evaluating the argument 'x' in selecting a method for function 'nInd': 
  no slot of name "strata" for this object of class "genind"

1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_that(nInd(popsub(partial_clone, 1)), equals(nInd(partial_clone[p1, ]))) at test-popsub.R:57
5: condition(object)
6: compare(expected, actual, ...)
7: nInd(partial_clone[p1, ])

l. Error: subsetting works with genclone objects ------------------------------------------
argument "tab" is missing, with no default
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: popsub(nancycats, c(4, 8), drop = FALSE) at test-popsub.R:69
5: is.genind(gid) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/data_subset.r:285
6: validObject(x)
7: anyStrings(validityMethod(as(object, superClass)))
8: validityMethod(as(object, superClass))
9: ncol(object@tab)
10: as(object, superClass)
11: asMethod(object)
12: new(structure("genind", package = "adegenet"))
13: initialize(value, ...)
14: initialize(value, ...)
15: .local(.Object, ...)
16: colnames(tab)
17: is.data.frame(x)

m. Error: Dissimilarity distance works as expected. ---------------------------------------
REAL() can only be applied to a 'numeric', not a 'integer'
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: diss.dist(nan1, mat = TRUE) at test-values.R:29
5: vapply(x, function(x) .Call("pairdiffs", x@tab) * (ploid/2), numeric(np)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/distances.r:109
6: FUN(X[[1L]], ...)

Testing poppr
Loading required package: adegenet
Loading required package: ade4
   ==========================
    adegenet 2.0.0 is loaded
   ==========================

 - to start: type '?adegenet'
 - to browse the adegenet website: type 'adegenetWeb()'
 - to post questions/comments: adegenet-forum@lists.r-forge.r-project.org
 - to report bugs, request features, contribute: http://goo.gl/dZuu5X


This is poppr version 1.1.4.99.89. To get started, type package?poppr
Amova tests : 12
Graph color conversion tests : ...
Population Distance Tests : ......
Errors and Exceptions : ...
Genclone coercion tests : ...................
Greyscale tests : ...
Data import tests : ..
Missing tests : ......
Multilocus genotype tests : ...............No multilocus genotypes were detected across populations
3No multilocus genotypes were detected across populations
4.........
Polyploid Tests : ....
Poppr table tests : ......................
Population subset tests : ..................................
Analytical value tests : ............


1. Error: Amova returns published values ---------------------------------------
NA/NaN argument
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: poppr.amova(Aeut, ~Pop/Subpop, quiet = TRUE) at test-amova.R:5
5: pool_haplotypes(x, dfname = dfname) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/amova.r:238
6: repool(separate_haplotypes(x)) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/internal.r:1417
7: separate_haplotypes(x)
8: which(1:geno_length%%(allele_length + 1) == 0) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/internal.r:1391

2. Error: AMOVA handles subsetted genclone objects -----------------------------
argument of length 0
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: poppr.amova(Athena, ~Subpop, quiet = TRUE) at test-amova.R:30
5: pool_haplotypes(x, dfname = dfname) at /Users/zhian/Documents/Grunwald/short-scripts/poppr/R/amova.r:238

3. Failure(@test-mlg.R#50): mlg.crosspop will work with subsetted genclone objects
x <- mlg.crosspop(Athena, quiet = TRUE) not equal to expected_output
Modes: list, numeric
names for target but not for current
Length mismatch: comparison on first 1 components
Component 1: names for target but not for current
Component 1: Numeric: lengths (2, 1) differ

4. Failure(@test-mlg.R#51): mlg.crosspop will work with subsetted genclone objects
y <- mlg.crosspop(Athena, indexreturn = TRUE) not equal to expected_mlgout
Numeric: lengths (6, 1) differ

There were 11 warnings (use warnings() to see them)