get_bio_fmt_specimens() has started failing
Closed this issue · 2 comments
tkelman commented
Maybe this issue should be opened on BioCore, but this is where it showed up on PkgEval as possibly the first package to start using that function.
| | |_| | | | (_| | | Version 0.6.1-pre.0 (2017-06-19 13:06 UTC)
_/ |\__'_|_|_|\__'_| | Commit dcf39a1* (30 days old release-0.6)
|__/ | x86_64-linux-gnu
julia> Pkg.init()
INFO: Initializing package repository /home/tkelman2/Julia/jlpkgtmp/v0.6
INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl
julia> Pkg.add("GeneticVariation")
INFO: Installing Automa v0.3.0
INFO: Installing BGZFStreams v0.1.4
INFO: Installing BioCore v1.2.0
INFO: Installing BioSequences v0.6.3
INFO: Installing BioSymbols v1.1.1
INFO: Installing BufferedStreams v0.3.3
INFO: Installing Combinatorics v0.4.1
INFO: Installing Compat v0.26.0
INFO: Installing DataStructures v0.6.0
INFO: Installing GeneticVariation v0.1.0
INFO: Installing IndexableBitVectors v0.1.2
INFO: Installing IntervalTrees v0.3.0
INFO: Installing IterTools v0.1.0
INFO: Installing Libz v0.2.4
INFO: Installing Polynomials v0.1.5
INFO: Installing Twiddle v0.4.0
INFO: Package database updated
julia> Pkg.test("GeneticVariation")
INFO: Computing test dependencies for GeneticVariation...
INFO: Installing Codecs v0.3.0
INFO: Installing YAML v0.2.1
INFO: Testing GeneticVariation
INFO: Compiling VCF parser...
Cloning into '/home/tkelman2/Julia/jlpkgtmp/v0.6/BioCore/BioFmtSpecimens'...
remote: Counting objects: 238, done.
remote: Compressing objects: 100% (176/176), done.
remote: Total 238 (delta 54), reused 223 (delta 54), pack-reused 0
Receiving objects: 100% (238/238), 2.25 MiB | 0 bytes/s, done.
Resolving deltas: 100% (54/54), done.
Checking connectivity... done.
fatal: reference is not a tree: 3140ef6110bb309703ffde564ce705eeb80607d4
ERROR: LoadError: failed process: Process(`git checkout 3140ef6110bb309703ffde564ce705eeb80607d4`, ProcessExited(128)) [128]
Stacktrace:
[1] pipeline_error(::Base.Process) at ./process.jl:682
[2] run(::Cmd) at ./process.jl:651
[3] cd(::BioCore.Testing.##1#2{String}, ::String) at ./file.jl:70
[4] get_bio_fmt_specimens(::String) at /home/tkelman2/Julia/jlpkgtmp/v0.6/BioCore/src/Testing.jl:16
[5] get_bio_fmt_specimens() at /home/tkelman2/Julia/jlpkgtmp/v0.6/BioCore/src/Testing.jl:12
[6] include_from_node1(::String) at ./loading.jl:569
[7] include(::String) at ./sysimg.jl:14
[8] process_options(::Base.JLOptions) at ./client.jl:305
[9] _start() at ./client.jl:371
while loading /home/tkelman2/Julia/jlpkgtmp/v0.6/GeneticVariation/test/runtests.jl, in expression starting on line 32
===============================[ ERROR: GeneticVariation ]================================
failed process: Process(`/home/tkelman2/Julia/julia-0.6/usr/bin/julia -Cx86-64 -J/home/tkelman2/Julia/julia-0.6/usr/lib/julia/sys.so --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes /home/tkelman2/Julia/jlpkgtmp/v0.6/GeneticVariation/test/runtests.jl`, ProcessExited(1)) [1]
==========================================================================================
INFO: Removing Codecs v0.3.0
INFO: Removing YAML v0.2.1
ERROR: GeneticVariation had test errors
TransGirlCodes commented
@tkelman I noticed this too, it had started happening a few days ago. I would have fixed it by now and have opened and issue and PR to do so in BioCore.jl, but today was my graduation and so the past two days have had only a few opportunities to log on, I'll resolve this issue tomorrow morning (uk).
tkelman commented
Oh I somehow didn't see BioJulia/BioCore.jl#6. Closing this as redundant.
Congrats!