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kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
https://kharchenkolab.github.io/Baysor/
MIT License
155 stars 31 forks source link

Build CLI from source error #50

Closed pvtodorov closed 1 year ago

pvtodorov commented 2 years ago

I am attempting to make the Baysor CLI from source without having Julia installed. I entered the commands on the front page of the repo

git clone https://github.com/kharchenkolab/Baysor.git
cd Baysor/bin
make

And produce the following trace

petar@/projects/petar/baysor_from_source/Baysor/bin$ make
make: Warning: File `Makefile' has modification time 26 s in the future
wget https://julialang-s3.julialang.org/bin/linux/x64/1.6/julia-1.6.4-linux-x86_64.tar.gz
--2022-08-02 14:27:24--  https://julialang-s3.julialang.org/bin/linux/x64/1.6/julia-1.6.4-linux-x86_64.tar.gz
Resolving julialang-s3.julialang.org (julialang-s3.julialang.org)... 151.101.2.49, 151.101.66.49, 151.101.130.49, ...
Connecting to julialang-s3.julialang.org (julialang-s3.julialang.org)|151.101.2.49|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 113341695 (108M) [application/x-tar]
Saving to: ‘julia-1.6.4-linux-x86_64.tar.gz’

100%[================================================================================================================================================================>] 113,341,695  215MB/s   in 0.5s

2022-08-02 14:27:25 (215 MB/s) - ‘julia-1.6.4-linux-x86_64.tar.gz’ saved [113341695/113341695]

rm -rf /nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4/
tar xf julia-1.6.4-linux-x86_64.tar.gz && touch /nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia_success
mkdir -p /nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/
echo 'empty!(DEPOT_PATH); push!(DEPOT_PATH, "/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/")' >> /nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//etc/julia/startup.jl
/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")); Pkg.add(Pkg.PackageSpec(name="PackageCompiler", version="2.0.2"));'
     Cloning git-repo `https://github.com/kharchenkolab/Baysor.git`
    Updating git-repo `https://github.com/kharchenkolab/Baysor.git`
   Resolving package versions...
julia version requirement for package `Baysor [cc9f9468]` not satisfied
  Installing known registries into `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/`

       Added registry `General` to `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/registries/General`
   Installed OpenEXR_jll ───────────────── v3.1.1+0
   Installed Glib_jll ──────────────────── v2.68.3+2
   Installed ImageQualityIndexes ───────── v0.3.3
   Installed PCRE_jll ──────────────────── v8.44.0+0
   Installed Formatting ────────────────── v0.4.2
   Installed LogExpFunctions ───────────── v0.3.17
   Installed PNGFiles ──────────────────── v0.3.16
   Installed FixedPointNumbers ─────────── v0.8.4
   Installed HDF5_jll ──────────────────── v1.12.2+1
   Installed x264_jll ──────────────────── v2021.5.5+0
   Installed DataValueInterfaces ───────── v1.0.0
   Installed NearestNeighborDescent ────── v0.3.5
   Installed Distributions ─────────────── v0.25.66
   Installed LaTeXStrings ──────────────── v1.3.0
   Installed IntegralArrays ────────────── v0.1.5
   Installed JSON ──────────────────────── v0.21.3
   Installed Vega ──────────────────────── v2.3.1
   Installed StructArrays ──────────────── v0.6.11
   Installed ConstructionBase ──────────── v1.4.0
   Installed MetaGraphs ────────────────── v0.7.1
   Installed libass_jll ────────────────── v0.15.1+0
   Installed OpenEXR ───────────────────── v0.3.2
   Installed ChangesOfVariables ────────── v0.1.4
   Installed TableTraitsUtils ──────────── v1.0.2
   Installed Xorg_libXext_jll ──────────── v1.3.4+4
   Installed OrderedCollections ────────── v1.4.1
   Installed MappedArrays ──────────────── v0.4.1
   Installed FFTViews ──────────────────── v0.3.2
   Installed Graphics ──────────────────── v1.1.2
   Installed HDF5 ──────────────────────── v0.16.10
   Installed ProgressMeter ─────────────── v1.7.2
   Installed StatsAPI ──────────────────── v1.2.2
   Installed Distances ─────────────────── v0.10.7
   Installed Inflate ───────────────────── v0.1.2
   Installed Gettext_jll ───────────────── v0.21.0+0
   Installed LoggingExtras ─────────────── v0.4.9
   Installed SIMD ──────────────────────── v3.4.1
   Installed TiffImages ────────────────── v0.6.0
   Installed Rmath_jll ─────────────────── v0.3.0+0
   Installed XML2_jll ──────────────────── v2.9.14+0
   Installed Calculus ──────────────────── v0.5.1
   Installed ImageTransformations ──────── v0.9.5
   Installed IntervalSets ──────────────── v0.7.1
   Installed ColorTypes ────────────────── v0.11.4
   Installed VoronoiDelaunay ───────────── v0.4.3
   Installed ImageShow ─────────────────── v0.3.6
   Installed Cairo ─────────────────────── v1.0.5
   Installed SignedDistanceFields ──────── v0.4.0
   Installed AxisArrays ────────────────── v0.4.6
   Installed PolygonOps ────────────────── v0.1.2
   Installed JpegTurbo_jll ─────────────── v2.1.2+0
   Installed Crayons ───────────────────── v4.1.1
   Installed libpng_jll ────────────────── v1.6.38+0
   Installed MbedTLS ───────────────────── v1.1.2
   Installed IteratorInterfaceExtensions ─ v1.0.0
   Installed ArrayInterfaceCore ────────── v0.1.16
   Installed CodecZlib ─────────────────── v0.7.0
   Installed LERC_jll ──────────────────── v3.0.0+1
   Installed Requires ──────────────────── v1.3.0
   Installed Netpbm ────────────────────── v1.0.2
   Installed ImageSegmentation ─────────── v1.7.0
   Installed Fontconfig_jll ────────────── v2.13.93+0
   Installed DensityInterface ──────────── v0.4.0
   Installed HypergeometricFunctions ───── v0.3.11
   Installed Parameters ────────────────── v0.12.3
   Installed QOI ───────────────────────── v1.0.0
   Installed InvertedIndices ───────────── v1.1.0
   Installed FreeType2_jll ─────────────── v2.10.4+0
   Installed SentinelArrays ────────────── v1.3.13
   Installed Xorg_libxcb_jll ───────────── v1.13.0+3
   Installed Opus_jll ──────────────────── v1.3.2+0
   Installed Xorg_libXdmcp_jll ─────────── v1.1.3+4
   Installed Preferences ───────────────── v1.3.0
   Installed FillArrays ────────────────── v0.13.2
   Installed InlineStrings ─────────────── v1.1.4
   Installed SpecialFunctions ──────────── v2.1.7
   Installed ScanByte ──────────────────── v0.3.3
   Installed Libtiff_jll ───────────────── v4.4.0+0
   Installed ImageBase ─────────────────── v0.1.5
   Installed Xorg_libXau_jll ───────────── v1.0.9+4
   Installed AbstractFFTs ──────────────── v1.2.1
   Installed URIs ──────────────────────── v1.4.0
   Installed RegionTrees ───────────────── v0.3.2
   Installed NodeJS ────────────────────── v1.3.0
   Installed CustomUnitRanges ──────────── v1.0.2
   Installed DiffResults ───────────────── v1.0.3
   Installed DiffRules ─────────────────── v1.11.0
   Installed GeometricalPredicates ─────── v0.4.2
   Installed ImageMetadata ─────────────── v0.9.8
   Installed JLD2 ──────────────────────── v0.4.22
   Installed RangeArrays ───────────────── v0.3.2
   Installed Graphs ────────────────────── v1.7.1
   Installed StatsBase ─────────────────── v0.33.20
   Installed Imath_jll ─────────────────── v3.1.2+0
   Installed Quaternions ───────────────── v0.5.6
   Installed FFMPEG ────────────────────── v0.4.1
   Installed ImageCore ─────────────────── v0.9.4
   Installed MosaicViews ───────────────── v0.3.3
   Installed ImageFiltering ────────────── v0.7.1
   Installed Pixman_jll ────────────────── v0.40.1+0
   Installed DataFrames ────────────────── v1.3.4
   Installed PkgVersion ────────────────── v0.1.1
   Installed UnPack ────────────────────── v1.0.2
   Installed IterTools ─────────────────── v1.4.0
   Installed OptimBase ─────────────────── v2.0.2
   Installed Sixel ─────────────────────── v0.1.2
   Installed Showoff ───────────────────── v1.0.3
   Installed OffsetArrays ──────────────── v1.12.7
   Installed LightGraphs ───────────────── v1.3.5
   Installed PaddedViews ───────────────── v0.5.11
   Installed Adapt ─────────────────────── v3.4.0
   Installed Libgpg_error_jll ──────────── v1.42.0+0
   Installed IndirectArrays ────────────── v1.0.0
   Installed ColorBrewer ───────────────── v0.4.0
   Installed AbstractTrees ─────────────── v0.4.2
   Installed MakieCore ─────────────────── v0.3.6
   Installed TensorCore ────────────────── v0.1.1
   Installed ImageMagick_jll ───────────── v6.9.10-12+3
   Installed Tables ────────────────────── v1.7.0
   Installed Packing ───────────────────── v0.4.2
   Installed Rmath ─────────────────────── v0.7.0
   Installed Automa ────────────────────── v0.8.2
   Installed Graphite2_jll ─────────────── v1.3.14+0
   Installed FFTW_jll ──────────────────── v3.3.10+0
   Installed Grisu ─────────────────────── v1.0.2
   Installed ArnoldiMethod ─────────────── v0.1.0
   Installed FreeType ──────────────────── v4.0.0
   Installed LZO_jll ───────────────────── v2.10.1+0
   Installed QuadGK ────────────────────── v2.4.2
   Installed PooledArrays ──────────────── v1.4.2
   Installed StackViews ────────────────── v0.1.1
   Installed x265_jll ──────────────────── v3.5.0+0
   Installed InverseFunctions ──────────── v0.1.7
   Installed libvorbis_jll ─────────────── v1.3.7+1
   Installed libsixel_jll ──────────────── v1.8.6+1
   Installed Missings ──────────────────── v1.0.2
   Installed Xorg_xtrans_jll ───────────── v1.4.0+3
   Installed MultivariateStats ─────────── v0.9.1
   Installed FFTW ──────────────────────── v1.5.0
   Installed StatsFuns ─────────────────── v1.0.1
   Installed DualNumbers ───────────────── v0.6.8
   Installed Bzip2_jll ─────────────────── v1.0.8+0
   Installed JpegTurbo ─────────────────── v0.1.1
   Installed WeakRefStrings ────────────── v1.4.2
   Installed SimpleTraits ──────────────── v0.9.4
   Installed StaticArraysCore ──────────── v1.0.1
   Installed OpenSSL_jll ───────────────── v1.1.17+0
   Installed MathTeXEngine ─────────────── v0.4.3
   Installed FriBidi_jll ───────────────── v1.0.10+0
   Installed DataStructures ────────────── v0.18.13
   Installed CoordinateTransformations ─── v0.6.2
   Installed RelocatableFolders ────────── v0.3.0
   Installed EarCut_jll ────────────────── v2.2.3+0
   Installed MacroTools ────────────────── v0.5.9
   Installed Xorg_libpthread_stubs_jll ─── v0.1.0+3
   Installed AxisAlgorithms ────────────── v1.0.1
   Installed DataAPI ───────────────────── v1.10.0
   Installed FiniteDiff ────────────────── v2.14.0
   Installed SimpleBufferStream ────────── v1.1.0
   Installed StaticArrays ──────────────── v1.5.2
   Installed LazyModules ───────────────── v0.3.1
   Installed FFMPEG_jll ────────────────── v4.4.2+0
   Installed NearestNeighbors ──────────── v0.4.11
   Installed CSV ───────────────────────── v0.10.4
   Installed Animations ────────────────── v0.4.1
   Installed ForwardDiff ───────────────── v0.10.30
   Installed IniFile ───────────────────── v0.5.1
   Installed NaNMath ───────────────────── v1.0.1
   Installed PlotUtils ─────────────────── v1.3.0
   Installed Libgcrypt_jll ─────────────── v1.8.7+0
   Installed Rotations ─────────────────── v1.3.1
   Installed URIParser ─────────────────── v0.4.1
   Installed Ogg_jll ───────────────────── v1.3.5+1
   Installed MAT ───────────────────────── v0.10.3
   Installed BufferedStreams ───────────── v1.1.0
   Installed ColorVectorSpace ──────────── v0.9.9
   Installed Compat ────────────────────── v3.45.0
   Installed CommonSubexpressions ──────── v0.3.0
   Installed Libuuid_jll ───────────────── v2.36.0+0
   Installed Parsers ───────────────────── v2.3.2
   Installed JLLWrappers ───────────────── v1.4.1
   Installed PDMats ────────────────────── v0.11.16
   Installed Libffi_jll ────────────────── v3.2.2+1
   Installed HTTP ──────────────────────── v1.2.0
   Installed SortingAlgorithms ─────────── v1.0.1
   Installed CairoMakie ────────────────── v0.8.12
   Installed FilePaths ─────────────────── v0.8.3
   Installed WoodburyMatrices ──────────── v0.5.5
   Installed Libiconv_jll ──────────────── v1.16.1+1
   Installed ComputationalResources ────── v0.3.2
   Installed LsqFit ────────────────────── v0.12.1
   Installed ArgParse ──────────────────── v1.1.4
   Installed NLSolversBase ─────────────── v7.8.2
   Installed Pango_jll ─────────────────── v1.50.3+0
   Installed ImageMagick ───────────────── v1.2.2
   Installed UMAP ──────────────────────── v0.1.9
   Installed ImageDistances ────────────── v0.2.16
   Installed Xorg_libXrender_jll ───────── v0.9.10+4
   Installed CatIndices ────────────────── v0.2.2
   Installed Contour ───────────────────── v0.6.2
   Installed GridLayoutBase ────────────── v0.9.0
   Installed libfdk_aac_jll ────────────── v2.0.2+0
   Installed Arpack ────────────────────── v0.5.3
   Installed FreeTypeAbstraction ───────── v0.9.9
   Installed Images ────────────────────── v0.25.2
   Installed isoband_jll ───────────────── v0.2.3+0
   Installed Cairo_jll ─────────────────── v1.16.1+1
   Installed ImageContrastAdjustment ───── v0.3.10
   Installed Xorg_libX11_jll ───────────── v1.6.9+4
   Installed Reexport ──────────────────── v1.2.2
   Installed ColorSchemes ──────────────── v3.19.0
   Installed Match ─────────────────────── v1.2.0
   Installed Zstd_jll ──────────────────── v1.5.2+0
   Installed Observables ───────────────── v0.5.1
   Installed DocStringExtensions ───────── v0.9.1
   Installed Clustering ────────────────── v0.14.2
   Installed IrrationalConstants ───────── v0.1.1
   Installed PrettyTables ──────────────── v1.3.1
   Installed Expat_jll ─────────────────── v2.4.8+0
   Installed Isoband ───────────────────── v0.1.1
   Installed UnicodeFun ────────────────── v0.4.1
   Installed Colors ────────────────────── v0.12.8
   Installed FilePathsBase ─────────────── v0.9.18
   Installed VegaLite ──────────────────── v2.6.0
   Installed GeometryBasics ────────────── v0.4.2
   Installed libaom_jll ────────────────── v3.4.0+0
   Installed SimpleWeightedGraphs ──────── v1.2.1
   Installed ImageMorphology ───────────── v0.3.2
   Installed TiledIteration ────────────── v0.3.1
   Installed JSONSchema ────────────────── v1.0.1
   Installed Ratios ────────────────────── v0.4.3
   Installed OpenSpecFun_jll ───────────── v0.5.5+0
   Installed TableTraits ───────────────── v1.0.1
   Installed HarfBuzz_jll ──────────────── v2.8.1+1
   Installed XSLT_jll ──────────────────── v1.1.34+0
   Installed Libmount_jll ──────────────── v2.35.0+0
   Installed DataValues ────────────────── v0.4.13
   Installed MKL_jll ───────────────────── v2022.0.0+0
   Installed Arpack_jll ────────────────── v3.5.0+3
   Installed CEnum ─────────────────────── v0.4.2
   Installed TextWrap ──────────────────── v1.0.1
   Installed LAME_jll ──────────────────── v3.100.1+0
   Installed ImageAxes ─────────────────── v0.6.10
   Installed FileIO ────────────────────── v1.15.0
   Installed IntelOpenMP_jll ───────────── v2018.0.3+2
   Installed Setfield ──────────────────── v1.0.0
   Installed ChainRulesCore ────────────── v1.15.3
   Installed KernelDensity ─────────────── v0.6.5
   Installed Makie ─────────────────────── v0.17.12
   Installed Scratch ───────────────────── v1.1.1
   Installed TranscodingStreams ────────── v0.9.6
   Installed ImageIO ───────────────────── v0.6.6
   Installed Interpolations ────────────── v0.14.3
  Downloaded artifact: OpenEXR
  Downloaded artifact: PCRE
  Downloaded artifact: Glib
  Downloaded artifact: HDF5
  Downloaded artifact: vegalite_app
  Downloaded artifact: x264
  Downloaded artifact: libass
  Downloaded artifact: Xorg_libXext
  Downloaded artifact: Gettext
  Downloaded artifact: Rmath
  Downloaded artifact: XML2
  Downloaded artifact: JpegTurbo
  Downloaded artifact: libpng
  Downloaded artifact: LERC
  Downloaded artifact: Fontconfig
  Downloaded artifact: FreeType2
  Downloaded artifact: Xorg_libxcb
  Downloaded artifact: Opus
  Downloaded artifact: Xorg_libXdmcp
  Downloaded artifact: Libtiff
  Downloaded artifact: Xorg_libXau
  Downloaded artifact: nodejs_app
  Downloaded artifact: Imath
  Downloaded artifact: Pixman
  Downloaded artifact: Libgpg_error
  Downloaded artifact: ImageMagick
  Downloaded artifact: Graphite2
  Downloaded artifact: FFTW
  Downloaded artifact: LZO
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  Downloaded artifact: libsixel
  Downloaded artifact: libvorbis
  Downloaded artifact: Xorg_xtrans
  Downloaded artifact: Bzip2
  Downloaded artifact: OpenSSL
  Downloaded artifact: FriBidi
  Downloaded artifact: EarCut
  Downloaded artifact: Xorg_libpthread_stubs
  Downloaded artifact: FFMPEG
  Downloaded artifact: Libgcrypt
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  Downloaded artifact: Libuuid
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  Downloaded artifact: Xorg_libXrender
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  Downloaded artifact: LAME
  Downloaded artifact: IntelOpenMP
    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Project.toml`
  [cc9f9468] + Baysor v0.5.2 `https://github.com/kharchenkolab/Baysor.git#master`
    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Manifest.toml`
  [621f4979] + AbstractFFTs v1.2.1
  [1520ce14] + AbstractTrees v0.4.2
  [79e6a3ab] + Adapt v3.4.0
  [27a7e980] + Animations v0.4.1
  [c7e460c6] + ArgParse v1.1.4
  [ec485272] + ArnoldiMethod v0.1.0
  [7d9fca2a] + Arpack v0.5.3
  [30b0a656] + ArrayInterfaceCore v0.1.16
  [67c07d97] + Automa v0.8.2
  [13072b0f] + AxisAlgorithms v1.0.1
  [39de3d68] + AxisArrays v0.4.6
  [cc9f9468] + Baysor v0.5.2 `https://github.com/kharchenkolab/Baysor.git#master`
  [e1450e63] + BufferedStreams v1.1.0
  [fa961155] + CEnum v0.4.2
  [336ed68f] + CSV v0.10.4
  [159f3aea] + Cairo v1.0.5
  [13f3f980] + CairoMakie v0.8.12
  [49dc2e85] + Calculus v0.5.1
  [aafaddc9] + CatIndices v0.2.2
  [d360d2e6] + ChainRulesCore v1.15.3
  [9e997f8a] + ChangesOfVariables v0.1.4
  [aaaa29a8] + Clustering v0.14.2
  [944b1d66] + CodecZlib v0.7.0
  [a2cac450] + ColorBrewer v0.4.0
  [35d6a980] + ColorSchemes v3.19.0
  [3da002f7] + ColorTypes v0.11.4
  [c3611d14] + ColorVectorSpace v0.9.9
  [5ae59095] + Colors v0.12.8
  [bbf7d656] + CommonSubexpressions v0.3.0
  [34da2185] + Compat v3.45.0
  [ed09eef8] + ComputationalResources v0.3.2
  [187b0558] + ConstructionBase v1.4.0
  [d38c429a] + Contour v0.6.2
  [150eb455] + CoordinateTransformations v0.6.2
  [a8cc5b0e] + Crayons v4.1.1
  [dc8bdbbb] + CustomUnitRanges v1.0.2
  [9a962f9c] + DataAPI v1.10.0
  [a93c6f00] + DataFrames v1.3.4
  [864edb3b] + DataStructures v0.18.13
  [e2d170a0] + DataValueInterfaces v1.0.0
  [e7dc6d0d] + DataValues v0.4.13
  [b429d917] + DensityInterface v0.4.0
  [163ba53b] + DiffResults v1.0.3
  [b552c78f] + DiffRules v1.11.0
  [b4f34e82] + Distances v0.10.7
  [31c24e10] + Distributions v0.25.66
  [ffbed154] + DocStringExtensions v0.9.1
  [fa6b7ba4] + DualNumbers v0.6.8
  [c87230d0] + FFMPEG v0.4.1
  [4f61f5a4] + FFTViews v0.3.2
  [7a1cc6ca] + FFTW v1.5.0
  [5789e2e9] + FileIO v1.15.0
  [8fc22ac5] + FilePaths v0.8.3
  [48062228] + FilePathsBase v0.9.18
  [1a297f60] + FillArrays v0.13.2
  [6a86dc24] + FiniteDiff v2.14.0
  [53c48c17] + FixedPointNumbers v0.8.4
  [59287772] + Formatting v0.4.2
  [f6369f11] + ForwardDiff v0.10.30
  [b38be410] + FreeType v4.0.0
  [663a7486] + FreeTypeAbstraction v0.9.9
  [fd0ad045] + GeometricalPredicates v0.4.2
  [5c1252a2] + GeometryBasics v0.4.2
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  [ae029012] + Requires v1.3.0
  [79098fc4] + Rmath v0.7.0
  [6038ab10] + Rotations v1.3.1
  [fdea26ae] + SIMD v3.4.1
  [7b38b023] + ScanByte v0.3.3
  [6c6a2e73] + Scratch v1.1.1
  [91c51154] + SentinelArrays v1.3.13
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  [699a6c99] + SimpleTraits v0.9.4
  [47aef6b3] + SimpleWeightedGraphs v1.2.1
  [45858cf5] + Sixel v0.1.2
  [a2af1166] + SortingAlgorithms v1.0.1
  [276daf66] + SpecialFunctions v2.1.7
  [cae243ae] + StackViews v0.1.1
  [90137ffa] + StaticArrays v1.5.2
  [1e83bf80] + StaticArraysCore v1.0.1
  [82ae8749] + StatsAPI v1.2.2
  [2913bbd2] + StatsBase v0.33.20
  [4c63d2b9] + StatsFuns v1.0.1
  [09ab397b] + StructArrays v0.6.11
  [3783bdb8] + TableTraits v1.0.1
  [382cd787] + TableTraitsUtils v1.0.2
  [bd369af6] + Tables v1.7.0
  [62fd8b95] + TensorCore v0.1.1
  [b718987f] + TextWrap v1.0.1
  [731e570b] + TiffImages v0.6.0
  [06e1c1a7] + TiledIteration v0.3.1
  [3bb67fe8] + TranscodingStreams v0.9.6
  [c4f8c510] + UMAP v0.1.9
  [30578b45] + URIParser v0.4.1
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  [239c3e63] + Vega v2.3.1
  [112f6efa] + VegaLite v2.6.0
  [72f80fcb] + VoronoiDelaunay v0.4.3
  [ea10d353] + WeakRefStrings v1.4.2
  [efce3f68] + WoodburyMatrices v0.5.5
  [68821587] + Arpack_jll v3.5.0+3
  [6e34b625] + Bzip2_jll v1.0.8+0
  [83423d85] + Cairo_jll v1.16.1+1
  [5ae413db] + EarCut_jll v2.2.3+0
  [2e619515] + Expat_jll v2.4.8+0
  [b22a6f82] + FFMPEG_jll v4.4.2+0
  [f5851436] + FFTW_jll v3.3.10+0
  [a3f928ae] + Fontconfig_jll v2.13.93+0
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  [7746bdde] + Glib_jll v2.68.3+2
  [3b182d85] + Graphite2_jll v1.3.14+0
  [0234f1f7] + HDF5_jll v1.12.2+1
  [2e76f6c2] + HarfBuzz_jll v2.8.1+1
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  [3f19e933] + p7zip_jll
    Building HDF5 → `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9ffc57b9bb643bf3fce34f3daf9ff506ed2d8b7a/build.log`
Precompiling project...
  260 dependencies successfully precompiled in 325 seconds
   Resolving package versions...
julia version requirement for package `Baysor [cc9f9468]` not satisfied
julia version requirement for package `Baysor [cc9f9468]` not satisfied
   Installed RelocatableFolders ─ v0.1.3
   Installed PackageCompiler ──── v2.0.2
    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Project.toml`
  [9b87118b] + PackageCompiler v2.0.2
    Updating `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/environments/v1.6/Manifest.toml`
  [9b87118b] + PackageCompiler v2.0.2
  [05181044] ↓ RelocatableFolders v0.3.0 ⇒ v0.1.3
Precompiling project...
  6 dependencies successfully precompiled in 283 seconds (255 already precompiled)
/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia -e 'using Pkg; Pkg.build(); using Baysor' && touch /nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia//deps_success
    Building HDF5 → `/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9ffc57b9bb643bf3fce34f3daf9ff506ed2d8b7a/build.log`
/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//bin/julia -e 'ENV["JULIA_DEPOT_PATH"]="/nfsdata/projects/petar/baysor_from_source/Baysor/bin/.julia/"; using PackageCompiler; import Pkg; Pkg.activate(".."); Pkg.instantiate(); import Baysor; create_sysimage(:Baysor; precompile_execution_file="$(dirname(pathof(Baysor)))/../bin/precompile.jl", sysimage_path="BaysorSysimage.so")'
  Activating environment at `/nfsdata/projects/petar/baysor_from_source/Baysor/Project.toml`
     Cloning git-repo `https://github.com/VPetukhov/Vega.jl`
     Cloning git-repo `https://github.com/queryverse/VegaLite.jl.git`
ERROR: The manifest file you are using was most likely generated by a different version of Julia and is not compatible with this Julia version
Stacktrace:
 [1] load_urls(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
   @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:545
 [2] #download_source#57
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:733 [inlined]
 [3] download_source
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:732 [inlined]
 [4] instantiate(ctx::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Base.BinaryPlatforms.Platform, allow_build::Bool, allow_autoprecomp::Bool, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1408
 [5] instantiate
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1325 [inlined]
 [6] #instantiate#252
   @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1321 [inlined]
 [7] instantiate()
   @ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1321
 [8] top-level scope
   @ none:1
make: *** [/nfsdata/projects/petar/baysor_from_source/Baysor/bin/julia-1.6.4//../BaysorSysimage.so] Error 1
bethrusnak commented 2 years ago

I have this same issue. The process downloads julia 1.6.4 but that seems to be a problem.

vhaghani26 commented 2 years ago

I am also having this problem. I cannot seem to install regardless of the method. I believe the dependencies are an issue, but I am not sure how to solve the issue

klprint commented 2 years ago

Same issue here

klprint commented 2 years ago

I am also having this problem. I cannot seem to install regardless of the method. I believe the dependencies are an issue, but I am not sure how to solve the issue

Regarding the install: I had issues with the installation, too (running on Ubuntu 18.04 server). I managed to install it with the following method:

  1. Download Julia 1.6.4 (as it is done automatically, when following the CLI tool compilation tutorial in the README)
  2. start the Julia REPL
  3. install Baysor using: 
    using Pkg
Pkg.add([PackageSpec(name="UMAP", rev="master"), PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")])

    This step will complain that Julia 1.6.4 is not the right version for Baysor. Here, the right version number in the documentation would be really helpful.

  4. Create a file called Baysor and add the following content to it: 
    
#!/{PATH to your julia 1.6.4 binary, which you used to install Baysor above}

import Baysor: run_cli run_cli()


Make this file executable: `chmod +x Baysor`

Now you can use the `Baysor` script you created before like the Baysor binary. For now, almost everything works in my hands.
VPetukhov commented 1 year ago

Hi everyone, The build process is much more transparent in v0.6.0, please see it here.