Seeing the following with recent version of bedtools:
11:09 $ prove -lrv t/BEDTools.t
t/BEDTools.t ..
1..423
ok 1 - make a default factory
ok 2 - default to command 'bam_to_bed'
ok 3 - make a factory using command 'annotate'
ok 4 - factory command for 'annotate' is correct
ok 5 - all available options for 'annotate'
ok 6 - available parameters for 'annotate'
ok 7 - available switches for 'annotate'
not ok 8 - get version for 'annotate'
# Failed test 'get version for 'annotate''
# at t/BEDTools.t line 211.
ok 9 - can run command 'annotate'
ok 10 - result files exists for command 'annotate'
ok 11 - can return output format for command 'annotate'
ok 12 - result claims to be in correct format for command 'annotate'
ok 13 - can return output file for command 'annotate'
ok 14 - file format of '/var/folders/h3/j6j2rjzd719djds1f6b9llrc0000gp/T/DwCA49vrX6/Em_aSbREwF.bed' consistent with claim for 'annotate'
ok 15 - can set want to IO object for command 'annotate'
ok 16 - can get the basic object result for command 'annotate'
ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO'
ok 18 - can get the specific object result for command 'annotate'
ok 19 - 'returned object is correct for command 'annotate'' isa 'Bio::SeqFeature::Collection'
ok 20 - correct number of features for command 'annotate'
ok 21 - make a factory using command 'fasta_from_bed'
ok 22 - factory command for 'fasta_from_bed' is correct
ok 23 - all available options for 'fasta_from_bed'
ok 24 - available parameters for 'fasta_from_bed'
ok 25 - available switches for 'fasta_from_bed'
not ok 26 - get version for 'fasta_from_bed'
# Failed test 'get version for 'fasta_from_bed''
# at t/BEDTools.t line 211.
ok 27 - can run command 'fasta_from_bed'
ok 28 - result files exists for command 'fasta_from_bed'
ok 29 - can return output format for command 'fasta_from_bed'
ok 30 - result claims to be in correct format for command 'fasta_from_bed'
ok 31 - can return output file for command 'fasta_from_bed'
ok 32 - file format consistent with claim for 'fasta_from_bed'
ok 33 - can set want to IO object for command 'fasta_from_bed'
ok 34 - can get the basic object result for command 'fasta_from_bed'
ok 35 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::Root::IO'
ok 36 - can get the specific object result for command 'fasta_from_bed'
ok 37 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::SeqIO'
ok 38 - correct number of sequences for command 'fasta_from_bed'
ok 39 - make a factory using command 'overlap'
ok 40 - factory command for 'overlap' is correct
ok 41 - all available options for 'overlap'
ok 42 - available parameters for 'overlap'
ok 43 - available switches for 'overlap'
not ok 44 - get version for 'overlap'
# Failed test 'get version for 'overlap''
# at t/BEDTools.t line 211.
ok 45 - can set parameter -columns => '2,3,5,6'
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: No executable!
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/cjfields/bioperl/bioperl-live/lib/Bio/Root/Root.pm:447
STACK: Bio::Tools::Run::BEDTools::run /Users/cjfields/bioperl/bioperl-run/lib/Bio/Tools/Run/BEDTools.pm:278
STACK: t/BEDTools.t:274
-----------------------------------------------------------
# Looks like your test exited with 2 just after 45.
Dubious, test returned 2 (wstat 512, 0x200)
Failed 381/423 subtests
Test Summary Report
-------------------
t/BEDTools.t (Wstat: 512 Tests: 45 Failed: 3)
Failed tests: 8, 26, 44
Non-zero exit status: 2
Parse errors: Bad plan. You planned 423 tests but ran 45.
Files=1, Tests=45, 8 wallclock secs ( 0.03 usr 0.01 sys + 0.79 cusr 4.45 csys = 5.28 CPU)
Result: FAIL
✘-1 ~/bioperl/bioperl-run [master|…3⚑ 2]
11:53 $ which bedtools
/usr/local/bin/bedtools
✘-1 ~/bioperl/bioperl-run [master|…3⚑ 2]
11:54 $ bedtools --version
bedtools v2.27.1
Seeing the following with recent version of bedtools: