Won't precompile (on RIS server), with or without graphics enabled

[ChantalJuntao]

Precompiling project...
  ✗ RegisterDeformation
  ✗ RegisterQD
  0 dependencies successfully precompiled in 45 seconds. 214 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

RegisterQD [ac24ea0c-1830-11e9-18d4-81f172323054]

Failed to precompile RegisterQD [ac24ea0c-1830-11e9-18d4-81f172323054] to "/storage1/fs1/holy/Active/chantal/.julia/compiled/v1.9/RegisterQD/jl_GqrhAG".
WARNING: could not import CoordinateTransformations.transform into RegisterDeformation
ERROR: LoadError: UndefVarError: `HDF5Dataset` not defined
Stacktrace:
 [1] top-level scope
   @ /storage1/fs1/holy/Active/chantal/.julia/packages/RegisterDeformation/IWvZQ/src/RegisterDeformation.jl:587
 [2] include
   @ ./Base.jl:457 [inlined]
 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
   @ Base ./loading.jl:2049
 [4] top-level scope
   @ stdin:3
in expression starting at /storage1/fs1/holy/Active/chantal/.julia/packages/RegisterDeformation/IWvZQ/src/RegisterDeformation.jl:1
in expression starting at stdin:3
ERROR: LoadError: Failed to precompile RegisterDeformation [c19381b7-cf49-59d7-881c-50dfbd227eaf] to "/storage1/fs1/holy/Active/chantal/.julia/compiled/v1.9/RegisterDeformation/jl_5oP09T".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2300
  [3] compilecache
    @ ./loading.jl:2167 [inlined]
  [4] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1805
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1660
  [6] macro expansion
    @ ./loading.jl:1648 [inlined]
  [7] macro expansion
    @ ./lock.jl:267 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1611
  [9] include
    @ ./Base.jl:457 [inlined]
 [10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2049
 [11] top-level scope
    @ stdin:3
in expression starting at /storage1/fs1/holy/Active/chantal/.julia/packages/RegisterQD/ZBH17/src/RegisterQD.jl:1
in expression starting at stdin:3

[ChantalJuntao]

Update turns out that I was using v0.2.0, because RegisterQD v0.3.1 is now holding back quite a few things:

add RegisterQD@0.3.1
   Resolving package versions...
    Updating `...Project.toml`
⌅ [02fcd773] ↓ ImageTransformations v0.10.0 ⇒ v0.9.5
⌅ [916415d5] ↓ Images v0.26.0 ⇒ v0.25.3
  [ac24ea0c] ↑ RegisterQD v0.2.0 ⇒ v0.3.1
    Updating `...Manifest.toml`
⌅ [787d08f9] ↓ ImageMorphology v0.4.5 ⇒ v0.3.2
⌅ [02fcd773] ↓ ImageTransformations v0.10.0 ⇒ v0.9.5
⌅ [916415d5] ↓ Images v0.26.0 ⇒ v0.25.3
⌅ [06e1c1a7] ↓ TiledIteration v0.5.0 ⇒ v0.3.1

[pywugate]

I think I also encountered similar problem.
I am new to use HolyLabRegistry, hope I configured it correctly.

should I create fork of these packages?

julia> pkglst = ["BlockRegistration", "RegisterMismatch", "RegisterQD", ]
julia> Pkg.add(pkglst)
Precompiling project...
  ✗ RegisterDeformation
  ✗ RegisterPenalty
  ✗ RegisterQD
  ✗ RegisterFit
  ✗ RegisterHindsight
  ✗ RegisterOptimize
  ✗ BlockRegistration
  18 dependencies successfully precompiled in 70 seconds. 224 already precompiled.
  7 dependencies errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`  

julia> err
PkgPrecompileError: The following 2 direct dependencies failed to precompile:

BlockRegistration [96be3cfc-dfc9-41f0-9424-fd41ed36fd5e]

Failed to precompile BlockRegistration [96be3cfc-dfc9-41f0-9424-fd41ed36fd5e] to "~\\.julia\\compiled\\v1.10\\BlockRegistration\\jl_114.tmp".
WARNING: could not import CoordinateTransformations.transform into RegisterDeformation
ERROR: LoadError: UndefVarError: `HDF5Dataset` not defined
Stacktrace:
 [1] top-level scope
   @ ~\.julia\packages\RegisterDeformation\IWvZQ\src\RegisterDeformation.jl:587
 [2] include
   @ .\Base.jl:495 [inlined]
 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
   @ Base .\loading.jl:2222
 [4] top-level scope
   @ stdin:3
in expression starting at ~\.julia\packages\RegisterDeformation\IWvZQ\src\RegisterDeformation.jl:1
in expression starting at stdin:3
ERROR: LoadError: Failed to precompile RegisterDeformation [c19381b7-cf49-59d7-881c-50dfbd227eaf] to "~\\.julia\\compiled\\v1.10\\RegisterDeformation\\jl_947.tmp".        
Stacktrace:
  [1] error(s::String)
    @ Base .\error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base .\loading.jl:2468
  [3] compilecache
    @ .\loading.jl:2340 [inlined]
  [4] (::Base.var"#968#969"{Base.PkgId})()
    @ Base .\loading.jl:1974
  [5] mkpidlock(f::Base.var"#968#969"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~\AppData\Local\Programs\Julia-1.10.2\share\julia\stdlib\v1.10\FileWatching\src\pidfile.jl:93
  [6] #mkpidlock#6
    @ ~\AppData\Local\Programs\Julia-1.10.2\share\julia\stdlib\v1.10\FileWatching\src\pidfile.jl:88 [inlined]
  [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~\AppData\Local\Programs\Julia-1.10.2\share\julia\stdlib\v1.10\FileWatching\src\pidfile.jl:111
  [8] #invokelatest#2
    @ .\essentials.jl:894 [inlined]
  [9] invokelatest
    @ .\essentials.jl:889 [inlined]
 [10] maybe_cachefile_lock(f::Base.var"#968#969"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; 
stale_age::Int64)
    @ Base .\loading.jl:2983
 [11] maybe_cachefile_lock
    @ .\loading.jl:2980 [inlined]
 [12] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:1970
 [13] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1812
 [14] #invoke_in_world#3
    @ .\essentials.jl:926 [inlined]
 [15] invoke_in_world
    @ .\essentials.jl:923 [inlined]
 [16] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1803
 [17] macro expansion
    @ .\loading.jl:1790 [inlined]
 [18] macro expansion
    @ .\lock.jl:267 [inlined]
 [19] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1753
 [20] #invoke_in_world#3
    @ .\essentials.jl:926 [inlined]
 [21] invoke_in_world
    @ .\essentials.jl:923 [inlined]
 [22] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1746
 [23] include
    @ .\Base.jl:495 [inlined]
 [24] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base .\loading.jl:2222
 [25] top-level scope
    @ stdin:3
in expression starting at ~\.julia\packages\BlockRegistration\mLYy8\src\BlockRegistration.jl:1
in expression starting at stdin:3
RegisterQD [ac24ea0c-1830-11e9-18d4-81f172323054]

Failed to precompile RegisterQD [ac24ea0c-1830-11e9-18d4-81f172323054] to "~\\.julia\\compiled\\v1.10\\RegisterQD\\jl_82D0.tmp".
WARNING: could not import CoordinateTransformations.transform into RegisterDeformation
ERROR: LoadError: UndefVarError: `HDF5Dataset` not defined
Stacktrace:
 [1] top-level scope
   @ ~\.julia\packages\RegisterDeformation\IWvZQ\src\RegisterDeformation.jl:587
 [2] include
   @ .\Base.jl:495 [inlined]
 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
   @ Base .\loading.jl:2222
 [4] top-level scope
   @ stdin:3
in expression starting at ~\.julia\packages\RegisterDeformation\IWvZQ\src\RegisterDeformation.jl:1
in expression starting at stdin:3
ERROR: LoadError: Failed to precompile RegisterDeformation [c19381b7-cf49-59d7-881c-50dfbd227eaf] to "~\\.julia\\compiled\\v1.10\\RegisterDeformation\\jl_9ACE.tmp".       
Stacktrace:
  [1] error(s::String)
    @ Base .\error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base .\loading.jl:2468
  [3] compilecache
    @ .\loading.jl:2340 [inlined]
  [4] (::Base.var"#968#969"{Base.PkgId})()
    @ Base .\loading.jl:1974
  [5] mkpidlock(f::Base.var"#968#969"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~\AppData\Local\Programs\Julia-1.10.2\share\julia\stdlib\v1.10\FileWatching\src\pidfile.jl:93
  [6] #mkpidlock#6
    @ ~\AppData\Local\Programs\Julia-1.10.2\share\julia\stdlib\v1.10\FileWatching\src\pidfile.jl:88 [inlined]
  [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~\AppData\Local\Programs\Julia-1.10.2\share\julia\stdlib\v1.10\FileWatching\src\pidfile.jl:111
  [8] #invokelatest#2
    @ .\essentials.jl:894 [inlined]
  [9] invokelatest
    @ .\essentials.jl:889 [inlined]
 [10] maybe_cachefile_lock(f::Base.var"#968#969"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; 
stale_age::Int64)
    @ Base .\loading.jl:2983
 [11] maybe_cachefile_lock
    @ .\loading.jl:2980 [inlined]
 [12] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:1970
 [13] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1812
 [14] #invoke_in_world#3
    @ .\essentials.jl:926 [inlined]
 [15] invoke_in_world
    @ .\essentials.jl:923 [inlined]
 [16] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1803
 [17] macro expansion
    @ .\loading.jl:1790 [inlined]
 [18] macro expansion
    @ .\lock.jl:267 [inlined]
 [19] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1753
 [20] #invoke_in_world#3
    @ .\essentials.jl:926 [inlined]
 [21] invoke_in_world
    @ .\essentials.jl:923 [inlined]
 [22] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1746
 [23] include
    @ .\Base.jl:495 [inlined]
 [24] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base .\loading.jl:2222
 [25] top-level scope
    @ stdin:3
in expression starting at ~\.julia\packages\RegisterQD\ZBH17\src\RegisterQD.jl:1
in expression starting at stdin:3

(registration) pkg> add RegisterQD@0.3.1
   Resolving package versions...
ERROR: Unsatisfiable requirements detected for package JLD2 [033835bb]:
 JLD2 [033835bb] log:
 ├─possible versions are: 0.1.0-0.4.46 or uninstalled
 ├─restricted by julia compatibility requirements to versions: 0.4.28-0.4.46 or uninstalled     
 └─restricted by compatibility requirements with RegisterDeformation [c19381b7] to versions: 0.1.0-0.1.14 — no versions left
   └─RegisterDeformation [c19381b7] log:
     ├─possible versions are: 0.1.0-0.4.7 or uninstalled
     ├─restricted by compatibility requirements with BlockRegistration [96be3cfc] to versions: 0.1.0-0.3.4
     │ └─BlockRegistration [96be3cfc] log:
     │   ├─possible versions are: 0.2.0-0.2.2 or uninstalled
     │   └─restricted to versions * by an explicit requirement, leaving only versions: 0.2.0-0.2.2
     └─restricted by compatibility requirements with RegisterQD [ac24ea0c] to versions: 0.3.0-0.4.7, leaving only versions: 0.3.0-0.3.4
       └─RegisterQD [ac24ea0c] log:
         ├─possible versions are: 0.1.0-0.3.2 or uninstalled
         └─restricted to versions 0.3.1 by an explicit requirement, leaving only versions: 0.3.1

(registration) pkg> up
    Updating registry at `~\.julia\registries\General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
    Updating registry at `~\.julia\registries\HolyLabRegistry`
    Updating git-repo `git@github.com:HolyLab/HolyLabRegistry.git`
  No Changes to `~\Documents\Julia\registration\Project.toml`
  No Changes to `~\Documents\Julia\registration\Manifest.toml`

julia> Pkg.status()
Status `~\Documents\Julia\registration\Project.toml`
  [96be3cfc] BlockRegistration v0.2.2
⌅ [3c0dd727] RegisterMismatch v0.3.3
⌃ [ac24ea0c] RegisterQD v0.2.0
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated`

julia> versioninfo()
Julia Version 1.10.2
Commit bd47eca2c8 (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: 16 × AMD Ryzen 7 4800HS with Radeon Graphics
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver2)
Threads: 6 default, 0 interactive, 3 GC (on 16 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS = 6