Bug#930548: julia: Arpack not building with source compiled (packaged) Julia

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Bug#930548: julia: Arpack not building with source compiled (packaged) Julia

mateusz.kaduk@gmail.com
Package: julia
Version: 1.1.0+dfsg-1
Severity: important

Dear Maintainer,

When I download Julia 1.1.0 from website, I can add Distributions package which depends on Arpack. However, with Debian's packaged Julia, Arpack is failing to build for some reason. To reproduce the issue ]add Distributions

Thanks for looking into this.
Mateusz

-- System Information:
Debian Release: 10.0
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.19.0-5-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages julia depends on:
ii  julia-common           1.1.0+dfsg-1
ii  libc6                  2.28-10
ii  libcholmod3            1:5.4.0+dfsg-1
ii  libcurl3-gnutls        7.64.0-3
ii  libdsfmt-19937-1       2.2.3+dfsg-4
ii  libgit2-27             0.27.7+dfsg.1-0.2
ii  libgmp10               2:6.1.2+dfsg-4
ii  libjulia1              1.1.0+dfsg-1
ii  libllvm6.0             1:6.0.1-11
ii  libmbedcrypto3         2.16.0-1
ii  libmbedtls12           2.16.0-1
ii  libmbedx509-0          2.16.0-1
ii  libmpfr6               4.0.2-1
ii  libopenblas-base       0.3.5+ds-3
ii  libopenlibm2           0.6.0+dfsg-2
ii  libpcre2-8-0           10.32-5
ii  libspqr2               1:5.4.0+dfsg-1
ii  libssh2-1              1.8.0-2.1
ii  libsuitesparseconfig5  1:5.4.0+dfsg-1
ii  libumfpack5            1:5.4.0+dfsg-1
ii  libunwind8             1.2.1-9
ii  libutf8proc2           2.3.0-1

Versions of packages julia recommends:
ii  git      1:2.20.1-2
ii  openssl  1.1.1c-1

Versions of packages julia suggests:
pn  ess        <none>
ii  julia-doc  1.1.0+dfsg-1
ii  vim-julia  0.0~git20190129.84104d0-1

-- no debconf information

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Bug#930548: julia: Arpack not building with source compiled (packaged) Julia

Graham Inggs-3
Control: found -1 1.0.3+dfsg-4
Control: tags -1 + confirmed

Hi Mateusz

I was able to reproduce this in 1.0.3+dfsg-4 and 1.0.4+dfsg-1.

Regards
Graham

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Bug#930548: julia: Arpack not building with source compiled (packaged) Julia

Graham Inggs-3
From ~/.julia/packages/Arpack/cu5By/deps after adding Distributions
using upstream's version 1.0.4:

[ Info: Downloading
https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc7.tar.gz
to /home/ginggs/.julia/packages/Arpack/cu5By/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc7.tar.gz...

From the same file using Debian's version 1.0.4+dfsg-1:

[ Info: Downloading
https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz
to /home/ginggs/.julia/packages/Arpack/cu5By/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz...
ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack,
"Prefix(/home/ginggs/.julia/packages/Arpack/cu5By/deps/usr)") is not
satisfied, cannot generate deps.jl!
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] #write_deps_file#152(::Bool, ::Function, ::String,
::Array{LibraryProduct,1}) at
/home/ginggs/.julia/packages/BinaryProvider/TcAwt/src/Products.jl:414
 [3] (::getfield(BinaryProvider,
Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}},
::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at
./none:0
 [4] top-level scope at none:0
 [5] include at ./boot.jl:317 [inlined]
 [6] include_relative(::Module, ::String) at ./loading.jl:1044
 [7] include(::Module, ::String) at ./sysimg.jl:29
 [8] include(::String) at ./client.jl:392
 [9] top-level scope at none:0
in expression starting at
/home/ginggs/.julia/packages/Arpack/cu5By/deps/build.jl:74

The only difference seems to be gcc7 vs gcc8 in the filename.
Using the Debian version, libarpack.so seems to be built successfully,
but there's a problem generating deps.jl.

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Bug#930548: julia: Arpack not building with source compiled (packaged) Julia

mateusz.kaduk@gmail.com
Looks like close to what we are seeing


They suggest using official binaries, that fixes one problem, but I run into another incompatibility with Debian libraries related to CUDA.
So if you don't need Debian's binaries like I do, official binaries should be a good temporal fix.

I tried manual Arpack build instructions from mentioned above new issue https://github.com/JuliaLinearAlgebra/Arpack.jl/pull/69 and I could build Arpack, but Julia is not picking it up.

On Sat, Jun 15, 2019 at 5:28 PM Graham Inggs <[hidden email]> wrote:
From ~/.julia/packages/Arpack/cu5By/deps after adding Distributions
using upstream's version 1.0.4:

[ Info: Downloading
https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc7.tar.gz
to /home/ginggs/.julia/packages/Arpack/cu5By/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc7.tar.gz...

From the same file using Debian's version 1.0.4+dfsg-1:

[ Info: Downloading
https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz
to /home/ginggs/.julia/packages/Arpack/cu5By/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz...
ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack,
"Prefix(/home/ginggs/.julia/packages/Arpack/cu5By/deps/usr)") is not
satisfied, cannot generate deps.jl!
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] #write_deps_file#152(::Bool, ::Function, ::String,
::Array{LibraryProduct,1}) at
/home/ginggs/.julia/packages/BinaryProvider/TcAwt/src/Products.jl:414
 [3] (::getfield(BinaryProvider,
Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}},
::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at
./none:0
 [4] top-level scope at none:0
 [5] include at ./boot.jl:317 [inlined]
 [6] include_relative(::Module, ::String) at ./loading.jl:1044
 [7] include(::Module, ::String) at ./sysimg.jl:29
 [8] include(::String) at ./client.jl:392
 [9] top-level scope at none:0
in expression starting at
/home/ginggs/.julia/packages/Arpack/cu5By/deps/build.jl:74

The only difference seems to be gcc7 vs gcc8 in the filename.
Using the Debian version, libarpack.so seems to be built successfully,
but there's a problem generating deps.jl.