rvosa / bio-phylo

Bio::Phylo - Phyloinformatic analysis using Perl
http://search.cpan.org/dist/Bio-Phylo
GNU General Public License v3.0
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Some tests fail if Statistics::R is installed #43

Open eserte opened 6 years ago

eserte commented 6 years ago

On a Debian/stretch system with various perl versions:

...
Problem while running this R command:
library("ape")

Error:
library("ape") : there is no package called 'ape'
Execution halted
t/50-replicate-tree.t .... skipped: (no reason given)
Problem while running this R command:
library("ape")

Error:
library("ape") : there is no package called 'ape'
Execution halted
t/51-replicate-binary.t .. skipped: (no reason given)
WARN Bio::Phylo::Matrices::MatrixRole::_replicate_dna [Bio/Phylo/Matrices/MatrixRole.pm 1323] - R package phylosim must be installed to replicate alignment.

#   Failed test at t/52-replicate-dna.t line 35.
# Looks like you failed 1 test of 1.
t/52-replicate-dna.t .....
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests
t/53-more-matrix.t ....... ok
t/54-rankprob.t .......... ok
WARN Bio::Phylo::Models::Substitution::Dna::modeltest [Bio/Phylo/Models/Substitution/Dna.pm 663] - modeltest not successful : Problem while running this R command:
data <- read.FASTA("/var/tmp/cpansmoker-1023/2018060206/T1oXmr8RYp")

Error:
could not find function "read.FASTA"
Execution halted

#   Failed test 'undef isa 'Bio::Phylo::Models::Substitution::Dna''
#   at t/55-modeltest.t line 37.
#     undef isn't defined
WARN Bio::Phylo::Models::Substitution::Dna::modeltest [Bio/Phylo/Models/Substitution/Dna.pm 663] - modeltest not successful : Problem while running this R command:
data <- read.FASTA("/var/tmp/cpansmoker-1023/2018060206/zgni7XrNLC")

Error:
could not find function "read.FASTA"
Execution halted

#   Failed test 'undef isa 'Bio::Phylo::Models::Substitution::Dna''
#   at t/55-modeltest.t line 41.
#     undef isn't defined
Can't call method "get_rate" on an undefined value at t/55-modeltest.t line 42, <DATA> line 1.
# Looks like your test exited with 25 just after 4.
t/55-modeltest.t .........
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 2/4 subtests
...

This happens only if Statistics::R is installed.