UndefVarError: FASTA not defined

[loki-phd]

Hello Garrett,

I am attempting to install Julia version of InformMe. fastaToCpG.jl, fails as BioSequences does not have a FASTA object associated with it. I originally thought that simply loading the BioSequences module in runtests.jl or fastaToCpG.jl will suffice, but the tests still failed. Can you possibly guide where we could modify the code to fix this issue and run InformMe?

I have attached the log from the command below.

test InformMe
    Testing InformMe
Status `/private/var/folders/sk/5sgxt4_s1m96d34nqddr8jr168q5zq/T/jl_tuvW21/Project.toml`
  [7e6ae17a] BioSequences v2.0.5
  [a134a8b2] BlackBoxOptim v0.5.0
  [717857b8] DSP v0.6.9
  [e30172f5] Documenter v0.25.5
  [5789e2e9] FileIO v1.4.4
  [6411b294] InformMe v0.1.0 `https://github.com/GarrettJenkinson/InformMe.jl#master`
  [033835bb] JLD2 v0.3.0
  [dae52e8d] QuadDIRECT v0.1.1 `https://github.com/timholy/QuadDIRECT.jl.git#master`
  [8ba89e20] Distributed
  [37e2e46d] LinearAlgebra
  [de0858da] Printf
  [9a3f8284] Random
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
Status `/private/var/folders/sk/5sgxt4_s1m96d34nqddr8jr168q5zq/T/jl_tuvW21/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [79e6a3ab] Adapt v2.3.0
  [56f22d72] Artifacts v1.3.0
  [67c07d97] Automa v0.8.0
  [47718e42] BioGenerics v0.1.0
  [7e6ae17a] BioSequences v2.0.5
  [3c28c6f8] BioSymbols v4.0.4
  [a134a8b2] BlackBoxOptim v0.5.0
  [a9c8d775] CPUTime v1.0.0
  [944b1d66] CodecZlib v0.7.0
  [861a8166] Combinatorics v1.0.2
  [34da2185] Compat v3.23.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.4+0
  [717857b8] DSP v0.6.9
  [9a962f9c] DataAPI v1.4.0
  [864edb3b] DataStructures v0.18.8
  [31c24e10] Distributions v0.23.12
  [ffbed154] DocStringExtensions v0.8.3
  [e30172f5] Documenter v0.25.5
  [e2ba6199] ExprTools v0.1.3
  [8f5d6c58] EzXML v1.1.0
  [7a1cc6ca] FFTW v1.2.4
  [f5851436] FFTW_jll v3.3.9+6
  [5789e2e9] FileIO v1.4.4
  [1a297f60] FillArrays v0.9.7
  [b5f81e59] IOCapture v0.1.1
  [1cb3b9ac] IndexableBitVectors v1.0.0
  [6411b294] InformMe v0.1.0 `https://github.com/GarrettJenkinson/InformMe.jl#master`
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [d8418881] Intervals v1.5.0
  [c8e1da08] IterTools v1.3.0
  [033835bb] JLD2 v0.3.0
  [692b3bcd] JLLWrappers v1.1.3
  [682c06a0] JSON v0.21.1
  [94ce4f54] Libiconv_jll v1.16.0+7
  [856f044c] MKL_jll v2020.2.254+0
  [1914dd2f] MacroTools v0.5.6
  [e1d29d7a] Missings v0.4.4
  [78c3b35d] Mocking v0.7.1
  [6fe1bfb0] OffsetArrays v1.4.0
  [efe28fd5] OpenSpecFun_jll v0.5.3+4
  [bac558e1] OrderedCollections v1.3.2
  [90014a1f] PDMats v0.10.1
  [69de0a69] Parsers v1.0.12
  [f27b6e38] Polynomials v1.1.12
  [85a6dd25] PositiveFactorizations v0.2.4
  [dae52e8d] QuadDIRECT v0.1.1 `https://github.com/timholy/QuadDIRECT.jl.git#master`
  [1fd47b50] QuadGK v2.4.1
  [3cdcf5f2] RecipesBase v1.1.1
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.1.1
  [79098fc4] Rmath v0.6.1
  [f50d1b31] Rmath_jll v0.2.2+1
  [a2af1166] SortingAlgorithms v0.3.1
  [d4ead438] SpatialIndexing v0.1.2
  [276daf66] SpecialFunctions v0.10.3
  [860ef19b] StableRNGs v0.1.2
  [90137ffa] StaticArrays v0.12.5
  [2913bbd2] StatsBase v0.33.2
  [4c63d2b9] StatsFuns v0.9.6
  [f269a46b] TimeZones v1.5.2
  [3bb67fe8] TranscodingStreams v0.9.5
  [7200193e] Twiddle v1.1.2
  [02c8fc9c] XML2_jll v2.9.10+3
  [83775a58] Zlib_jll v1.2.11+18
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [4607b0f0] SuiteSparse
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
Test Summary:  | Pass  Total
Test Core Algs |   28     28
Test Larger Functions: Error During Test at /Users/gp444/.julia/packages/InformMe/5Rkri/test/runtests.jl:125
  Got exception outside of a @test
  **_UndefVarError: FASTA not defined_**
  Stacktrace:
   [1] getproperty at ./Base.jl:26 [inlined]
   [2] fastaToCpG(::String; outdir::String, wsize::Int64) at /Users/gp444/.julia/packages/InformMe/5Rkri/src/fastaToCpG.jl:93
   [3] top-level scope at /Users/gp444/.julia/packages/InformMe/5Rkri/test/runtests.jl:193
   [4] top-level scope at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1115
   [5] top-level scope at /Users/gp444/.julia/packages/InformMe/5Rkri/test/runtests.jl:127
   [6] include(::String) at ./client.jl:457
   [7] top-level scope at none:6
   [8] eval(::Module, ::Any) at ./boot.jl:331
   [9] exec_options(::Base.JLOptions) at ./client.jl:272
   [10] _start() at ./client.jl:506
  
Test Summary:         | Pass  Error  Total
Test Larger Functions |    8      1      9
ERROR: LoadError: Some tests did not pass: 8 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /Users/gp444/.julia/packages/InformMe/5Rkri/test/runtests.jl:125
ERROR: Package InformMe errored during testing

[emarti88]

Hello Garrett,

This is Eduardo writing from the Feinberg lab. We are trying to use the julia version of informME an I had the exact same issue when running the test for installation.

Do you have any thoughts?

Eduardo

[GarrettJenkinson]

Hi all, sorry just seeing this issue now. Looks to me like it is a simple matter of versioning because the tests all passed when I originally wrote the code (badge icon still indicates the last build passed)....,i.e., I wrote this package three years ago but now it seems the dependencies of my dependencies have "moved on" and thus broken things here. Option 1 is to try to look at the dependencies such as BioSequences and see if you can install/peg your version to whatever they released 3 years ago. Option 2 is to try to modernize the code base to use newer versions of those repos. Option 3 is to use the matlab version of informMe.

As of last week, I have changed careers and thus do not have bandwidth to maintain informME any longer, but if someone wants to make a PR to fix this codebase, I would be happy to merge it to the main branch.

[emarti88]

Thanks, Garrett!

Is there a document here on the informME github that has the list of all the dependencies and their respective versions (Option 1)?

[GarrettJenkinson]

Yup, you can find it here:

https://github.com/GarrettJenkinson/InformMe.jl/blob/master/Project.toml

Hope you can get it working!

[GarrettJenkinson]

Also I did take a closer look at the error message and took a quick stab at fixing it in the tests. Let me know if it resolved your problem (unclear why the issue would have cropped up after passing tests originally, but think the change I made could conceivably resolve it).

[GarrettJenkinson]

Well the attempted fix and then reverted change did tell me the tests are still passing: https://app.travis-ci.com/github/GarrettJenkinson/InformMe.jl/jobs/578451514

One point of note, however, is that the tests are passing using Julia version 1.3. I would suggest using that version rather than a more recent iteration, just in case that is a source of the incompatibility. Also the test was run in a linux system, so if you are attempting to use windows or something else that might be part of the source of the discrepancy. Hope this information helps.

[emarti88]

Got it. I managed to pass the test using the exact commands you used here :
https://app.travis-ci.com/github/GarrettJenkinson/InformMe.jl/jobs/578451514

Hopefully I can get it to work on some of our own data.

Thanks!