Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

elynx-tree-0.7.2.0 test suite failure #6996

Closed
DanBurton opened this issue Jun 3, 2023 · 4 comments · Fixed by #7011
Closed

elynx-tree-0.7.2.0 test suite failure #6996

DanBurton opened this issue Jun 3, 2023 · 4 comments · Fixed by #7011

Comments

@DanBurton
Copy link
Contributor

Not sure if this is related to QuickCheck-2.14.3, deepseq-1.4.8.1, or something else.

       TestSuiteFailure (PackageIdentifier {pkgName = PackageName "elynx-tree"
, pkgVersion = mkVersion [0,7,2,0]}) (fromList [("tree-test",Just (ExitFailure
 1))]) (Just "/var/stackage/work/unpack-dir/.stack-work/logs/elynx-tree-0.7.2.
0-test.log") "\nELynx.Topology.Rooted\n  Topology\n    has reasonable applicat
ive take right instance [\226\156\148]\n      +++ OK, passed 100 tests.\n    h
as reasonable applicative take left instance [\226\156\148]\n      +++ OK, pas
sed 100 tests.\n    has reasonable applicative liftA2 instance [\226\156\148]\
n      +++ OK, passed 100 tests.\n    has reasonable applicative and functor i
nstances [\226\156\148]\n      +++ OK, passed 100 tests.\n    Functor\n      I
dentity [\226\156\148]\n        +++ OK, passed 100 tests.\n      Composition [
\226\156\148]\n        +++ OK, passed 100 tests.\n      Const [\226\156\148]\n
        +++ OK, passed 100 tests.\n    Foldable\n      fold [\226\156\148]\n
      +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n        +++ OK,
 passed 100 tests.\n      foldr [\226\156\148]\n        +++ OK, passed 100 tes
ts.\n      foldr' [\226\156\148]\n        +++ OK, passed 100 tests.\n      fol
dl [\226\156\148]\n        +++ OK, passed 100 tests.\n      foldl' [\226\156\1
48]\n        +++ OK, passed 100 tests.\n      foldl1 [\226\156\148]\n        +
++ OK, passed 100 tests.\n      foldr1 [\226\156\148]\n        +++ OK, passed
100 tests.\n      toList [\226\156\148]\n        +++ OK, passed 100 tests.\n
    null [\226\156\148]\n        +++ OK, passed 100 tests.\n      length [\226
\156\148]\n        +++ OK, passed 100 tests.\n    Traversable\n      Naturalit
y [\226\156\148]\n        +++ OK, passed 100 tests.\n      Identity [\226\156\
148]\n        +++ OK, passed 100 tests.\n      Composition [\226\156\148]\n
     +++ OK, passed 100 tests.\n      Sequence Naturality [\226\156\148]\n
    +++ OK, passed 100 tests.\n      Sequence Identity [\226\156\148]\n
 +++ OK, passed 100 tests.\n      Sequence Composition [\226\156\148]\n
 +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n        +++ OK, pass
ed 100 tests.\n      fmap [\226\156\148]\n        +++ OK, passed 100 tests.\n
   Applicative\n      Identity [\226\156\148]\n        +++ OK, passed 100 test
s.\n      Composition [\226\156\148]\n        +++ OK, passed 100 tests.\n
 Homomorphism [\226\156\148]\n        +++ OK, passed 100 tests.\n      Interch
ange [\226\156\148]\n        +++ OK, passed 100 tests.\n      LiftA2 Part 1 [\
226\156\148]\n        +++ OK, passed 100 tests.\n    Monad\n      Left Identit
y [\226\156\148]\n        +++ OK, passed 100 tests.\n      Right Identity [\22
6\156\148]\n        +++ OK, passed 100 tests.\n      Associativity [\226\156\1
48]\n        +++ OK, passed 100 tests.\n      Return [\226\156\148]\n        +
++ OK, passed 100 tests.\n      Ap [\226\156\148]\n        +++ OK, passed 100
tests.\nELynx.Tree.Bipartition\n  bipartitions\n    calculates correct biparti
tions for sample trees [\226\156\148]\n  bipartitionToBranch\n    creates a ma
p from bipartitions to branch lengths [\226\156\148]\nELynx.Tree.Distance\n  s
ymmetric\n    calculates correct distances for sample trees [\226\156\148]\n
  is zero for a collection of random trees [\226\156\152]\n  incompatibleSplit
\n    calculates correct distances for sample trees [\226\156\148]\n    calcul
ates correct distances for sample trees with branch support [\226\156\148]\n
  is zero for a collection of random trees [\226\156\152]\n  branchScore\n
calculates correct distances for sample trees [\226\156\148]\n    is zero for
a collection of random trees [\226\156\152]\nELynx.Tree.Export.Newick\n  parse
ByteStringWith newick $ toNewickPhyloByteString\n    should be an invariant fo
r a sample tree [\226\156\148]\n    should be an invariant for a sample tree [
\226\156\148]\n      +++ OK, passed 100 tests.\nELynx.Tree.Export.Nexus\n  toN
exusTrees\n    exports a nexus file with a TREES block [\226\156\148]\nELynx.T
ree.Import.Newick\n  newick\n    parses newick trees [\226\156\148]\n    parse
s a weird newick tree without node labels nor branch lengths [\226\156\148]\n
 newickRevBayes\n    parses newick trees in RevBayes format [\226\156\148]\nEL
ynx.Tree.Import.Nexus\n  trees\n    parses a nexus file with a TREES block [\2
26\156\148]\nELynx.Tree.Partition\n  partitions\n    calculates correct partit
ions for a sample tree [\226\156\148]\nELynx.Tree.Phylogeny\n  equal\n    corr
ectly handles some test cases [\226\156\148]\n    is commutative [\226\156\148
]\n      +++ OK, passed 100 tests.\n  roots\n    correctly handles leaves and
cherries [\226\156\148]\n    correctly handles simple trees [\226\156\148]\n
  returns the correct number of rooted trees for arbitrary trees [\226\156\148
]\n      +++ OK, passed 100 tests.\n    does not change the total tree length
[\226\156\148]\n      +++ OK, passed 100 tests.\n  outgroup\n    correctly han
dles simple trees [\226\156\148]\nELynx.Tree.Rooted\n  Tree\n    [Applicative]
 Reasonable take right instance [\226\156\148]\n      +++ OK, passed 100 tests
.\n    [Applicative] Reasonable take left instance [\226\156\148]\n      +++ O
K, passed 100 tests.\n    [Applicative] Reasonable liftA2 instance [\226\156\1
48]\n      +++ OK, passed 100 tests.\n    [Functor/Applicative] Reasonable fma
p/pure functions [\226\156\148]\n      +++ OK, passed 100 tests.\n    Functor\
n      Identity [\226\156\148]\n        +++ OK, passed 100 tests.\n      Compo
sition [\226\156\148]\n        +++ OK, passed 100 tests.\n      Const [\226\15
6\148]\n        +++ OK, passed 100 tests.\n    Bifunctor\n      Identity [\226
\156\148]\n        +++ OK, passed 100 tests.\n      First Identity [\226\156\1
48]\n        +++ OK, passed 100 tests.\n      Second Identity [\226\156\148]\n
        +++ OK, passed 100 tests.\n      Bifunctor Composition [\226\156\148]\
n        +++ OK, passed 100 tests.\n    Foldable\n      fold [\226\156\148]\n
       +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n        +++ OK
, passed 100 tests.\n      foldr [\226\156\148]\n        +++ OK, passed 100 te
sts.\n      foldr' [\226\156\148]\n        +++ OK, passed 100 tests.\n      fo
ldl [\226\156\148]\n        +++ OK, passed 100 tests.\n      foldl' [\226\156\
148]\n        +++ OK, passed 100 tests.\n      foldl1 [\226\156\148]\n
+++ OK, passed 100 tests.\n      foldr1 [\226\156\148]\n        +++ OK, passed
 100 tests.\n      toList [\226\156\148]\n        +++ OK, passed 100 tests.\n
     null [\226\156\148]\n        +++ OK, passed 100 tests.\n      length [\22
6\156\148]\n        +++ OK, passed 100 tests.\n    Bifoldable\n      Bifold Id
entity [\226\156\148]\n        +++ OK, passed 100 tests.\n      BifoldMap Iden
tity [\226\156\148]\n        +++ OK, passed 100 tests.\n      Bifoldr Identity
 [\226\156\148]\n        +++ OK, passed 100 tests.\n    Traversable\n      Nat
urality [\226\156\148]\n        +++ OK, passed 100 tests.\n      Identity [\22
6\156\148]\n        +++ OK, passed 100 tests.\n      Composition [\226\156\148
]\n        +++ OK, passed 100 tests.\n      Sequence Naturality [\226\156\148]
\n        +++ OK, passed 100 tests.\n      Sequence Identity [\226\156\148]\n
       +++ OK, passed 100 tests.\n      Sequence Composition [\226\156\148]\n
       +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n        +++ OK
, passed 100 tests.\n      fmap [\226\156\148]\n        +++ OK, passed 100 tes
ts.\n    Bitraversable\n      Naturality [\226\156\148]\n        +++ OK, passe
d 100 tests.\n      Identity [\226\156\148]\n        +++ OK, passed 100 tests.
\n      Composition [\226\156\148]\n        +++ OK, passed 100 tests.\n    App
licative\n      Identity [\226\156\148]\n        +++ OK, passed 100 tests.\n
    Composition [\226\156\148]\n        +++ OK, passed 100 tests.\n      Homom
orphism [\226\156\148]\n        +++ OK, passed 100 tests.\n      Interchange [
\226\156\148]\n        +++ OK, passed 100 tests.\n      LiftA2 Part 1 [\226\15
6\148]\n        +++ OK, passed 100 tests.\n    Monad\n      Left Identity [\22
6\156\148]\n        +++ OK, passed 100 tests.\n      Right Identity [\226\156\
148]\n        +++ OK, passed 100 tests.\n      Associativity [\226\156\148]\n
       +++ OK, passed 100 tests.\n      Return [\226\156\148]\n        +++ OK,
 passed 100 tests.\n      Ap [\226\156\148]\n        +++ OK, passed 100 tests.
\n  BranchTree\n    [Functor] Treats branches correctly with fmap [\226\156\14
8]\n      +++ OK, passed 100 tests.\n    [Traversable] Equal traversable insta
nce as Tree [\226\156\148]\n      +++ OK, passed 100 tests.\n    [Applicative]
 Reasonable take right instance [\226\156\148]\n      +++ OK, passed 100 tests
.\n    [Applicative] Reasonable take left instance [\226\156\148]\n      +++ O
K, passed 100 tests.\n    [Applicative] Reasonable liftA2 instance [\226\156\1
48]\n      +++ OK, passed 100 tests.\n    [Functor/Applicative] Reasonable fma
p/pure functions [\226\156\148]\n      +++ OK, passed 100 tests.\n    Functor\
n      Identity [\226\156\148]\n        +++ OK, passed 100 tests.\n      Compo
sition [\226\156\148]\n        +++ OK, passed 100 tests.\n      Const [\226\15
6\148]\n        +++ OK, passed 100 tests.\n    Foldable\n      fold [\226\156\
148]\n        +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n
 +++ OK, passed 100 tests.\n      foldr [\226\156\148]\n        +++ OK, passed
 100 tests.\n      foldr' [\226\156\148]\n        +++ OK, passed 100 tests.\n
     foldl [\226\156\148]\n        +++ OK, passed 100 tests.\n      foldl' [\2
26\156\148]\n        +++ OK, passed 100 tests.\n      foldl1 [\226\156\148]\n
       +++ OK, passed 100 tests.\n      foldr1 [\226\156\148]\n        +++ OK,
 passed 100 tests.\n      toList [\226\156\148]\n        +++ OK, passed 100 te
sts.\n      null [\226\156\148]\n        +++ OK, passed 100 tests.\n      leng
th [\226\156\148]\n        +++ OK, passed 100 tests.\n    Traversable\n      N
aturality [\226\156\148]\n        +++ OK, passed 100 tests.\n      Identity [\
226\156\148]\n        +++ OK, passed 100 tests.\n      Composition [\226\156\1
48]\n        +++ OK, passed 100 tests.\n      Sequence Naturality [\226\156\14
8]\n        +++ OK, passed 100 tests.\n      Sequence Identity [\226\156\148]\
n        +++ OK, passed 100 tests.\n      Sequence Composition [\226\156\148]\
n        +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n        +++
OK, passed 100 tests.\n      fmap [\226\156\148]\n        +++ OK, passed 100 t
ests.\n    Applicative\n      Identity [\226\156\148]\n        +++ OK, passed
100 tests.\n      Composition [\226\156\148]\n        +++ OK, passed 100 tests
.\n      Homomorphism [\226\156\148]\n        +++ OK, passed 100 tests.\n
 Interchange [\226\156\148]\n        +++ OK, passed 100 tests.\n      LiftA2 P
art 1 [\226\156\148]\n        +++ OK, passed 100 tests.\n  ZipTree\n    [Appli
cative] Reasonable take right instance [\226\156\148]\n      +++ OK, passed 10
0 tests.\n    [Applicative] Reasonable take left instance [\226\156\148]\n
  +++ OK, passed 100 tests.\n    [Applicative] Reasonable liftA2 instance [\22
6\156\148]\n      +++ OK, passed 100 tests.\n    [Functor/Applicative] Reasona
ble fmap/pure functions [\226\156\148]\n      +++ OK, passed 100 tests.\n    F
unctor\n      Identity [\226\156\148]\n        +++ OK, passed 100 tests.\n
  Composition [\226\156\148]\n        +++ OK, passed 100 tests.\n      Const [
\226\156\148]\n        +++ OK, passed 100 tests.\n    Foldable\n      fold [\2
26\156\148]\n        +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n
        +++ OK, passed 100 tests.\n      foldr [\226\156\148]\n        +++ OK,
 passed 100 tests.\n      foldr' [\226\156\148]\n        +++ OK, passed 100 te
sts.\n      foldl [\226\156\148]\n        +++ OK, passed 100 tests.\n      fol
dl' [\226\156\148]\n        +++ OK, passed 100 tests.\n      foldl1 [\226\156\
148]\n        +++ OK, passed 100 tests.\n      foldr1 [\226\156\148]\n
+++ OK, passed 100 tests.\n      toList [\226\156\148]\n        +++ OK, passed
 100 tests.\n      null [\226\156\148]\n        +++ OK, passed 100 tests.\n
   length [\226\156\148]\n        +++ OK, passed 100 tests.\n    Traversable\n
      Naturality [\226\156\148]\n        +++ OK, passed 100 tests.\n      Iden
tity [\226\156\148]\n        +++ OK, passed 100 tests.\n      Composition [\22
6\156\148]\n        +++ OK, passed 100 tests.\n      Sequence Naturality [\226
\156\148]\n        +++ OK, passed 100 tests.\n      Sequence Identity [\226\15
6\148]\n        +++ OK, passed 100 tests.\n      Sequence Composition [\226\15
6\148]\n        +++ OK, passed 100 tests.\n      foldMap [\226\156\148]\n
   +++ OK, passed 100 tests.\n      fmap [\226\156\148]\n        +++ OK, passe
d 100 tests.\n    Applicative\n      Identity [\226\156\148]\n        +++ OK,
passed 100 tests.\n      Composition [\226\156\148]\n        +++ OK, passed 10
0 tests.\n      Interchange [\226\156\148]\n        +++ OK, passed 100 tests.\
n      LiftA2 Part 1 [\226\156\148]\n        +++ OK, passed 100 tests.\n  ZipB
ranchTree\n    [Applicative] Reasonable take right instance [\226\156\148]\n
    +++ OK, passed 100 tests.\n    [Applicative] Reasonable take left instance
 [\226\156\148]\n      +++ OK, passed 100 tests.\n    [Applicative] Reasonable
 liftA2 instance [\226\156\148]\n      +++ OK, passed 100 tests.\n    [Functor
/Applicative] Reasonable fmap/pure functions [\226\156\148]\n      +++ OK, pas
sed 100 tests.\n    Functor\n      Identity [\226\156\148]\n        +++ OK, pa
ssed 100 tests.\n      Composition [\226\156\148]\n        +++ OK, passed 100
tests.\n      Const [\226\156\148]\n        +++ OK, passed 100 tests.\n    Fol
dable\n      fold [\226\156\148]\n        +++ OK, passed 100 tests.\n      fol
dMap [\226\156\148]\n        +++ OK, passed 100 tests.\n      foldr [\226\156\
148]\n        +++ OK, passed 100 tests.\n      foldr' [\226\156\148]\n
+++ OK, passed 100 tests.\n      foldl [\226\156\148]\n        +++ OK, passed
100 tests.\n      foldl' [\226\156\148]\n        +++ OK, passed 100 tests.\n
    foldl1 [\226\156\148]\n        +++ OK, passed 100 tests.\n      foldr1 [\2
26\156\148]\n        +++ OK, passed 100 tests.\n      toList [\226\156\148]\n
       +++ OK, passed 100 tests.\n      null [\226\156\148]\n        +++ OK, p
assed 100 tests.\n      length [\226\156\148]\n        +++ OK, passed 100 test
s.\n    Traversable\n      Naturality [\226\156\148]\n        +++ OK, passed 1
00 tests.\n      Identity [\226\156\148]\n        +++ OK, passed 100 tests.\n
     Composition [\226\156\148]\n        +++ OK, passed 100 tests.\n      Sequ
ence Naturality [\226\156\148]\n        +++ OK, passed 100 tests.\n      Seque
nce Identity [\226\156\148]\n        +++ OK, passed 100 tests.\n      Sequence
 Composition [\226\156\148]\n        +++ OK, passed 100 tests.\n      foldMap
[\226\156\148]\n        +++ OK, passed 100 tests.\n      fmap [\226\156\148]\n
        +++ OK, passed 100 tests.\n    Applicative\n      Identity [\226\156\1
48]\n        +++ OK, passed 100 tests.\n      Composition [\226\156\148]\n
    +++ OK, passed 100 tests.\n      Interchange [\226\156\148]\n        +++ O
K, passed 100 tests.\n      LiftA2 Part 1 [\226\156\148]\n        +++ OK, pass
ed 100 tests.\n  ZipTree and ZipBranchTree\n    [Applicative] Somewhat corresp
onding instances of <*> [\226\156\148]\n      +++ OK, passed 100 tests.\n    [
Traversable] Somewhat correspnding instances of traverse [\226\156\148]\n
 +++ OK, passed 100 tests.\n  prune\n    leaves a normal tree untouched [\226\
156\148]\n    correctly prunes a small example [\226\156\148]\n    leaves heig
ht constant for trees with branch lengths [\226\156\148]\n  dropLeavesWith\n
  returns the same tree if no leaves satisfy predicate [\226\156\148]\n    ret
urns nothing if all leaves satisfy predicate [\226\156\148]\n    returns the c
orrect subtree for a small example [\226\156\148]\nELynx.Tree.Support\n  colla
pse\n    creates a star tree for 1.0 [\226\156\148]\n\nFailures:\n\n  test/ELy
nx/Tree/DistanceSpec.hs:218:5: \n  1) ELynx.Tree.Distance.symmetric is zero fo
r a collection of random trees\n       Falsified (after 3 tests):\n         No
de {branch = Phylo {pBranchLength = Just (Length {fromLength = 3.7812069512529
387}), pBranchSupport = Just (Support {fromSupport = 23.0})}, label = 0.492147
15765426165, forest = [Node {branch = Phylo {pBranchLength = Just (Length {fro
mLength = 3.724989519695287e-2}), pBranchSupport = Just (Support {fromSupport
= 35.0})}, label = 0.0, forest = [Node {branch = Phylo {pBranchLength = Just (
Length {fromLength = 8.639341806782712}), pBranchSupport = Just (Support {from
Support = 76.0})}, label = 1.0, forest = []},Node {branch = Phylo {pBranchLeng
th = Just (Length {fromLength = 0.5274532644983732}), pBranchSupport = Just (S
upport {fromSupport = 33.0})}, label = 1.0, forest = []}]}]}\n\n  To rerun use
: --match \"/ELynx.Tree.Distance/symmetric/is zero for a collection of random
trees/\"\n\n  test/ELynx/Tree/DistanceSpec.hs:245:5: \n  2) ELynx.Tree.Distanc
e.incompatibleSplit is zero for a collection of random trees\n       Falsified
 (after 3 tests):\n         Node {branch = Phylo {pBranchLength = Just (Length
 {fromLength = 3.7812069512529387}), pBranchSupport = Just (Support {fromSuppo
rt = 23.0})}, label = 0.49214715765426165, forest = [Node {branch = Phylo {pBr
anchLength = Just (Length {fromLength = 3.724989519695287e-2}), pBranchSupport
 = Just (Support {fromSupport = 35.0})}, label = 0.0, forest = [Node {branch =
 gth {fromLength = 1.5}, label = 0.49214715765426165, forest = [Node {branch =
Length {fromLength = 0.6075058419150065}, label = 0.0, forest = [Node {branch
= Length {fromLength = 1.0}, label = 1.0, forest = []},Node {branch = Length {
fromLength = 1.0}, label = 1.0, forest = []}]}]}\n\n  To rerun use: --match \"
/ELynx.Tree.Distance/branchScore/is zero for a collection of random trees/\"\n
\nRandomized with seed 1107398630\n\nFinished in 12.1214 seconds\n208 examples
, 3 failures\n"
DanBurton added a commit that referenced this issue Jun 3, 2023
@DanBurton
expect test failure for elinx-tree per #6996
98a5d29
@DanBurton
Copy link
Contributor Author

Ping @dschrempf - I marked elynx-tree as an expected test failure in the stackage nightly build until this issue is addressed.

@dschrempf
Copy link
Contributor

Hi! Thanks for pinging me, I will have a look asap.

@dschrempf
Copy link
Contributor

Hi. This should be fixed in 0.7.2.1. How long should I wait until I remove the expected test fail from build-constraints.yaml?

@dschrempf dschrempf mentioned this issue Jun 15, 2023
Merged
@juhp
Copy link
Contributor

juhp commented Jun 16, 2023

Opening a PR request here anytime shortly after release should be sufficient

dschrempf added a commit to dschrempf/stackage that referenced this issue Jun 17, 2023
@dschrempf
remove expected test suite failure of elynx-tree
d784eb7 
- was fixed in elynx-tree version 0.7.2.1
- fixes commercialhaskell#6996
@dschrempf dschrempf mentioned this issue Jun 17, 2023
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

remove expected test suite failure of elynx-tree dschrempf/stackage
3 participants
@juhp @DanBurton @dschrempf