Precompiling failure for Singular

[wagh]

I have Ubuntu 21.10. I have installed julia from the official download page -- Generic Linux x86.

When I try julia> using Pkg; Pkg.add("Singular") julia> using Singular I am getting an error, probably with libsingular (error log attached).

Am I missing something?

-- VInay

julia-install-error.txt

[thofma]

Could you post the output of

julia> import Pkg; Pkg.status(mode=Pkg.PKGMODE_MANIFEST)

here? Thanks

[wagh]

Here is the required o/p:

        julia> import Pkg; Pkg.status(mode=Pkg.PKGMODE_MANIFEST)
        Status `~/.julia/environments/v1.8/Manifest.toml`
        ⌅ [c3fe647b] AbstractAlgebra v0.16.0
          [b99e7846] BinaryProvider v0.5.10
        ⌅ [1f15a43c] CxxWrap v0.11.2
        ⌅ [ffbed154] DocStringExtensions v0.8.6
        ⌅ [c863536a] GAP v0.5.2
          [e39c9192] GroebnerBasis v0.3.3
        ⌅ [3e1990a7] Hecke v0.10.5
          [692b3bcd] JLLWrappers v1.4.1
          [682c06a0] JSON v0.21.3
        ⌅ [472f376f] LoadFlint v0.5.1
          [1914dd2f] MacroTools v0.5.10
        ⌅ [4fe8b98c] Mongoc v0.6.2
        ⌅ [2edaba10] Nemo v0.22.1
        ⌃ [f1435218] Oscar v0.5.2
          [69de0a69] Parsers v2.5.5
        ⌅ [d720cf60] Polymake v0.5.6
          [21216c6a] Preferences v1.3.0
          [fb686558] RandomExtensions v0.4.3
          [ae029012] Requires v1.3.0
        ⌅ [bcd08a7b] Singular v0.5.2
          [66db9d55] SnoopPrecompile v1.0.3
          [90137ffa] StaticArrays v1.5.12
          [1e83bf80] StaticArraysCore v1.4.0
        ⌅ [e21ec000] Antic_jll v0.200.400+0
        ⌅ [d9960996] Arb_jll v200.1900.1+0
        ⌅ [e134572f] FLINT_jll v200.700.100+0
        ⌅ [5cd7a574] GAP_jll v400.1100.100+0
        ⌅ [de1ad85e] GAP_lib_jll v400.1100.100+0
          [e8aa6df9] GLPK_jll v5.0.1+0
          [dd4b983a] LZO_jll v2.10.1+0
          [90100e71] MongoC_jll v1.19.1+0
          [68e3532b] Ncurses_jll v6.2.0+0
          [76642167] Ninja_jll v1.11.1+0
          [458c3c95] OpenSSL_jll v1.1.19+0
          [80dd9cbb] PPL_jll v1.2.1+0
        ⌅ [83958c19] Perl_jll v5.30.3+2
          [05236dd9] Readline_jll v8.1.1+1
        ⌅ [43d676ae] Singular_jll v402.0.104+0
          [3161d3a3] Zstd_jll v1.5.2+0
        ⌅ [508c9074] bliss_jll v0.73.1+0
        ⌅ [28df3c45] boost_jll v1.71.0+3
          [f07e07eb] cddlib_jll v0.94.13+0
          [006bdf2e] gb_jll v0.17.0+0
          [1493ae25] lib4ti2_jll v1.6.10+0
        ⌅ [3eaa8342] libcxxwrap_julia_jll v0.8.8+1
        ⌅ [4d8266f6] libpolymake_julia_jll v0.4.117+0
        ⌅ [ae4fbd8f] libsingular_julia_jll v0.9.205+0
        ⌅ [3873f7d0] lrslib_jll v0.2.0+0
          [55c6dc9b] nauty_jll v2.6.13+0
        ⌅ [6690c6e9] normaliz_jll v300.800.901+0
        ⌅ [7c209550] polymake_jll v400.400.0+1
          [fe1e1685] snappy_jll v1.1.9+1
          [0dad84c5] ArgTools v1.1.1
          [56f22d72] Artifacts
          [2a0f44e3] Base64
          [ade2ca70] Dates
          [8ba89e20] Distributed
          [f43a241f] Downloads v1.6.0
          [7b1f6079] FileWatching
          [b77e0a4c] InteractiveUtils
          [b27032c2] LibCURL v0.6.3
          [76f85450] LibGit2
          [8f399da3] Libdl
          [37e2e46d] LinearAlgebra
          [56ddb016] Logging
          [d6f4376e] Markdown
          [a63ad114] Mmap
          [ca575930] NetworkOptions v1.2.0
          [44cfe95a] Pkg v1.8.0
          [de0858da] Printf
          [9abbd945] Profile
          [3fa0cd96] REPL
          [9a3f8284] Random
          [ea8e919c] SHA v0.7.0
          [9e88b42a] Serialization
          [6462fe0b] Sockets
          [2f01184e] SparseArrays
          [10745b16] Statistics
          [fa267f1f] TOML v1.0.0
          [a4e569a6] Tar v1.10.1
          [8dfed614] Test
          [cf7118a7] UUIDs
          [4ec0a83e] Unicode
          [e66e0078] CompilerSupportLibraries_jll v1.0.1+0
          [781609d7] GMP_jll v6.2.1+2
          [deac9b47] LibCURL_jll v7.84.0+0
          [29816b5a] LibSSH2_jll v1.10.2+0
          [3a97d323] MPFR_jll v4.1.1+1
          [c8ffd9c3] MbedTLS_jll v2.28.0+0
          [14a3606d] MozillaCACerts_jll v2022.2.1
          [4536629a] OpenBLAS_jll v0.3.20+0
          [83775a58] Zlib_jll v1.2.12+3
          [8e850b90] libblastrampoline_jll v5.1.1+0
          [8e850ede] nghttp2_jll v1.48.0+0
          [3f19e933] p7zip_jll v17.4.0+0
        Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

[fingolfin]

You have heavily outdated versions of all packages installed.

Try doing Pkg.update().

It is possible this won't do anything due to conflicting version requirements. In that case I recommend that you remove all packages from tye global Julia environment and then reinstall only those you really use

[wagh]

@fingolfin as you expected, Pkg.update() didnt help!

I wonder how these "outdated" packages were installed, as I had a fresh installation of julia and then packages were installed using Pkg.add(...). If this standard process installs outdated and also a few extra packages, then I guess this is also a bug(?) at some level.

[fingolfin]

You probably did not delete your ~/.julia directory so it wasn't a fully "fresh" installation

[thofma]

Before deleting ~/.julia, what does

julia> Pkg.pkg"add Oscar@0.11.2"

say? Only the error is interesting.

[wagh]

Sorry, I have already deleted... :-(. Now the "fresh" installation seems to have stuck at precompiling Singular.

Another experiment I did: On the fresh installation of Julia, I did Pkg.add( "Sigular" ). It works perfectly.

Then by removing the ~/.julia, I had another "fresh" installation. ON this I did Pkg.add( "GroebnerBasis" ). -- at this, the system is taking almost forever to precompile Singular. Edit: Forgot to mention, after Pkg.add( "Singular" ), if I give Pkg.add( "GroebnerBasis" ), it is still stuck at precompiling Singular.

The first time when I reported this, I had added GroebnerBasis before SIngular.

So now I wonder if the problem is at Singular OR GroebnerBasis!

[thofma]

GroebnerBasis has not been updated in years. If you want to use it, you are forced to use an old version of everything else (which might be broken on julia 1.8).

[wagh]

Ah, that explains! I think I will simply stick to "Singular" for now. As there is no problem with Pkg.add( "Singular" ), I will close this issue.

The "fresh" installation is still installing outdated packages. Can this be taken care of?