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bicycle1885 / CellFishing.jl

Fast and scalable cell search tool
MIT License
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Cannot run CellFishing #4

Closed bonohu closed 5 years ago

bonohu commented 5 years ago

After the installation, I tried to run CellFishing with the command below.

% julia -e 'using Pkg; Pkg.test("CellFishing")'

I came across the error. Below is the error message. I'm using macOS10.13.6 with Julia Version 1.0.1 (2018-09-29).

Test Summary: | Pass  Error  Total
CellIndex     |    7      1      8
ERROR: LoadError: Some tests did not pass: 7 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /Users/bono/.julia/packages/CellFishing/gilgp/test/runtests.jl:107
ERROR: Package CellFishing errored during testing
Stacktrace:
 [1] pkgerror(::String, ::Vararg{String,N} where N) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:120
 [2] macro expansion at ./logging.jl:313 [inlined]
 [3] #test#61(::Bool, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1284
 [4] #test at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:0 [inlined]
 [5] #test#42(::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:273
 [6] test at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:258 [inlined]
 [7] #test#41 at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:255 [inlined]
 [8] test at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:255 [inlined]
 [9] #test#40 at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:254 [inlined]
 [10] test at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:254 [inlined]
 [11] #test#39 at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:253 [inlined]
 [12] test(::String) at /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:253
 [13] top-level scope at none:0
bicycle1885 commented 5 years ago

I think this line (https://github.com/bicycle1885/CellFishing.jl/blob/1952d04b166e83d014317ca8510eaa21bbd21ab7/test/runtests.jl#L126) fails because it depends on the zstd command. The easiest solution to pass all the tests would be to install zstd, but this is an optional feature and will be removed in the next version. So, if you don't care, this is not problematic in practice.

bonohu commented 5 years ago

After install zstd, all tests were passed! Thanks for your comment.