homalg-project / homalgproject.jl Goto Github PK

Add the Graphviz_jll since Digraphs does not download and compile the Graphviz binaries.

Now that oscar-system/GAP.jl#413 has been merged start using GAP.Packages.install.

I recommend that in your scripts which invoke 4ti2 via Julia, you add --startup-file=no to the julia commands, to avoid issues (including errors and slowdowns) caused by user's startup files. While at it, perhaps also add in -O0 for a potential minor speedup.

See also oscar-system/Singular.jl#235 where similar scripts are added. (Perhaps we can eventually upgrade lib4ti2_jll to directly include these, but that's besides the point)

Moreover, I caution that these scripts may not work correctly in general, as there is no reason to assume that the user has lib4ti2_jll installed in their global environment. I.e. if I do Pkg.add("HomalgProject") then lib4ti2_jll will be available, but importing it from e.g. your graver script will fail (I think -- but I didn't try it. Please double check my claims ;-). I described a potential solution at oscar-system/Singular.jl#236

(Follow-up of #66)

The readme currently links to the Oscar installation page (https://oscar.computeralgebra.de/install/), which does not mention libjulia-dev. Maybe we should link to https://homalg-project.github.io/docs/installation instead (as in the readme of CapAndHomalg.jl)?

Or maybe the Oscar installation page should mention libjulia-dev? It seems to be required by GAP.jl, see oscar-system/GAP.jl#533.

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Add the lib4ti2_jll contributed by @fingolfin since 4ti2Interface does not download and compile the 4ti2 binaries.

I open this issue on behalf of F. Patrick Rabarison. Here is his original (email) message:

I'm a new user in julia and I have some trouble while using both the packages CapAndHomalg and HomalgProject. Maybe you could be any help? I use ubuntu 20.04 and here I send for instance what I got when using the package HomalgProject.

julia> using Pkg
julia> using HomalgProject
[ Info: Precompiling HomalgProject [50bd374c-87b5-11e9-015a-2febe71398bd]
[ Info: Set up gaproot at /home/rabarison/.julia/packages/GAP/wIHfC/gaproot/v1.4
ERROR: LoadError: could not load library "libjulia"
libjulia.so: cannot open shared object file: No such file or directory
Stacktrace:
[1] dlopen(::String, ::UInt32; throw_error::Bool) at
/build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Libdl/src/Libdl.jl:109
[2] dlopen at /build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Libdl/src/Libdl.jl:109
[inlined] (repeats 2 times)
[3] dlpath(::String) at
/build/julia-98cBbp/julia-1.4.1+dfsg/usr/share/julia/stdlib/v1.4/Libdl/src/Libdl.jl:232
[4] libDir() at ./string:32
[5] ldflags at ./string:52 [inlined]
[6] regenerate_gaproot() at
/home/rabarison/.julia/packages/GAP/wIHfC/src/setup.jl:89
[7] top-level scope at /home/rabarison/.julia/packages/GAP/wIHfC/src/GAP.jl:12
[8] include(::Module, ::String) at ./Base.jl:377
[9] top-level scope at none:2
[10] eval at ./boot.jl:331 [inlined]
[11] eval(::Expr) at ./client.jl:449
[12] top-level scope at ./none:3
in expression starting at
/home/rabarison/.julia/packages/GAP/wIHfC/src/GAP.jl:12
ERROR: LoadError: Failed to precompile GAP
[c863536a-3901-11e9-33e7-d5cd0df7b904] to
/home/rabarison/.julia/compiled/v1.4/GAP/YqHod_aVfVz.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922
[6] include(::Module, ::String) at ./Base.jl:377
[7] top-level scope at none:2
[8] eval at ./boot.jl:331 [inlined]
[9] eval(::Expr) at ./client.jl:449
[10] top-level scope at ./none:3
in expression starting at
/home/rabarison/.julia/packages/HomalgProject/tWdpO/src/HomalgProject.jl:65
ERROR: Failed to precompile HomalgProject
[50bd374c-87b5-11e9-015a-2febe71398bd] to
/home/rabarison/.julia/compiled/v1.4/HomalgProject/z4ehp_aVfVz.ji.
Stacktrace:
[1] error(::String) at ./error.jl:33
[2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
[3] _require(::Base.PkgId) at ./loading.jl:1029
[4] require(::Base.PkgId) at ./loading.jl:927
[5] require(::Module, ::Symbol) at ./loading.jl:922

Use the exported functions of ExecutableProducts to properly set the appropriate environment variables as suggest by @fingolfin.

Testing HomalgProject.jl with the master branch of GAP and either the master branch of Julia (commit 24efaa4f38) or Julia 1.2.0 rc2 fails when testing using Pkg.test("HomalgProject"). In contrast, when testing by running julia test/runtests.jl tests pass.

Here is the relevant debug output:

$ julia-1.2.0-rc2
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.2.0-rc2.0 (2019-07-08)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> import Pkg

julia> Pkg.test("HomalgProject")
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
   Testing HomalgProject
 Resolving package versions...
    Status `/tmp/jl_EVvG19/Manifest.toml`
  [c863536a] GAP v0.2.0
  [cd4130c4] GAPTypes v1.0.0
  [50bd374c] HomalgProject v0.1.6 [`~/.julia/dev/HomalgProject.jl`]
  [2a0f44e3] Base64  [`@stdlib/Base64`]
  [ade2ca70] Dates  [`@stdlib/Dates`]
  [8ba89e20] Distributed  [`@stdlib/Distributed`]
  [b77e0a4c] InteractiveUtils  [`@stdlib/InteractiveUtils`]
  [76f85450] LibGit2  [`@stdlib/LibGit2`]
  [8f399da3] Libdl  [`@stdlib/Libdl`]
  [56ddb016] Logging  [`@stdlib/Logging`]
  [d6f4376e] Markdown  [`@stdlib/Markdown`]
  [44cfe95a] Pkg  [`@stdlib/Pkg`]
  [de0858da] Printf  [`@stdlib/Printf`]
  [3fa0cd96] REPL  [`@stdlib/REPL`]
  [9a3f8284] Random  [`@stdlib/Random`]
  [ea8e919c] SHA  [`@stdlib/SHA`]
  [9e88b42a] Serialization  [`@stdlib/Serialization`]
  [6462fe0b] Sockets  [`@stdlib/Sockets`]
  [8dfed614] Test  [`@stdlib/Test`]
  [cf7118a7] UUIDs  [`@stdlib/UUIDs`]
  [4ec0a83e] Unicode  [`@stdlib/Unicode`]
Adding path /home/florian/.julia/packages/GAP/4IqsC/gap/.libs to DL_LOAD_PATH
Panic in src/julia_gc.c:825: could not import GAPTypes module into Julia
ERROR: LoadError: Failed to precompile HomalgProject [50bd374c-87b5-11e9-015a-2febe71398bd] to /home/florian/.julia/compiled/v1.2/HomalgProject/z4ehp.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1253
 [3] _require(::Base.PkgId) at ./loading.jl:1013
 [4] require(::Base.PkgId) at ./loading.jl:911
 [5] require(::Module, ::Symbol) at ./loading.jl:906
 [6] include at ./boot.jl:328 [inlined]
 [7] include_relative(::Module, ::String) at ./loading.jl:1094
 [8] include(::Module, ::String) at ./Base.jl:31
 [9] include(::String) at ./client.jl:431
 [10] top-level scope at none:5
in expression starting at /home/florian/.julia/dev/HomalgProject.jl/test/runtests.jl:1
ERROR: Package HomalgProject errored during testing
Stacktrace:
 [1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Types.jl:112
 [2] #test#119(::Bool, ::Nothing, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Operations.jl:1288
 [3] #test at ./none:0 [inlined]
 [4] #test#62(::Bool, ::Nothing, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:245
 [5] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:233 [inlined]
 [6] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
 [7] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
 [8] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
 [9] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
 [10] #test#59(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
 [11] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
 [12] top-level scope at REPL[2]:1

Tests for GAP.jl with Pkg.test("GAP") pass.

@rbehrends, @fingolfin, @sebasguts: Any ideas?

@fingolfin: Why do I get this warning when using HomalgProject but not when using Oscar although both import GAP and Singular.

julia> using HomalgProject
┌ Warning: More than one copy of gmp already loaded, using the 1st one
└ @ LoadFlint ~/.julia/packages/LoadFlint/42zpR/src/LoadFlint.jl:40

julia>