tkelman
commented
8 years ago what's your Pkg.status() ?
Closed rsrock closed 8 years ago
tkelman
commented
8 years ago what's your Pkg.status() ?
rsrock
commented
8 years ago Constantly changing, but currently
julia> Pkg.status()
93 required packages:
- ASCIIPlots 0.0.3
- AffineTransforms 0.1.4
- AndorSIF 0.0.3
- AppleAccelerate 0.2.1
- ArgParse 0.3.1
- Atom 0.4.4
- Autoreload 0.2.0
- BaseTestNext 0.2.2
- BenchmarkTools 0.0.3
- BioSeq 0.4.0
- Bootstrap 1.0.0
- Cairo 0.2.34
- Changepoints 0.2.0
- Clang 0.1.0
- Clustering 0.6.0
- ColorVectorSpace 0.1.6
- Colors 0.6.6
- Compat 0.8.6
- Compose 0.4.2+ master
- Coverage 0.3.0
- DSP 0.0.11
- DataArrays 0.3.8
- DataFrames 0.7.8
- Dates 0.4.4
- DecisionTree 0.4.2
- DeclarativePackages 0.1.2
- Dierckx 0.1.9
- Distances 0.3.2
- Distributions 0.10.2
- DocOpt 0.1.3
- Documenter 0.2.0
- FactCheck 0.4.3
- FastaIO 0.1.5
- GR 0.14.0
- Gadfly 0.4.2+ f46f74ac (dirty)
- Gallium 0.0.3
- Gillespie 0.0.1
- Graphics 0.1.3
- Grid 0.4.2
- Gtk 0.10.1
- HDF5 0.6.5
- HypothesisTests 0.3.0
- IJulia 1.2.0
- IProfile 0.4.0
- ImageMagick 0.1.7
- ImageView 0.1.20
- Images 0.5.8
- Immerse 0.0.11
- Interact 0.3.1
- JLD 0.6.3
- JSON 0.6.0
- LightXML 0.3.0
- Lint 0.2.4
- Logging 0.2.0
- LsqFit 0.0.2
- MacroTools 0.3.2
- Match 0.2.2
- Mustache 0.0.15
- NBInclude 1.0.1
- NLopt 0.3.2
- Netpbm 0.1.0
- NullableArrays 0.0.7
- NumericExtensions 0.6.2
- OpenGL 2.0.3
- Optim 0.5.0
- PGFPlots 1.3.5
- Patchwork 0.2.2
- PkgDev 0.1.2
- PlotlyJS 0.3.1
- Plots 0.9.0
- Polynomials 0.0.5
- ProfileView 0.1.3
- ProgressMeter 0.3.3
- PyCall 1.7.0
- PyPlot 2.2.1
- QuartzImageIO 0.1.4 master
- RCall 0.5.1
- RDatasets 0.1.3
- SIUnits 0.0.6
- StatsBase 0.9.0
- StrPack 0.0.1
- StructsOfArrays 0.0.3
- TerminalExtensions 0.1.0
- TestImages 0.1.1
- TextPlots 0.3.0
- TimeSeries 0.5.10
- Tk 0.3.8
- TypeCheck 0.0.3
- UnicodePlots 0.1.4
- Watcher 0.1.0
- Winston 0.11.13
- YAML 0.1.10
- ZMQ 0.3.4
98 additional packages:
- ASTInterpreter 0.0.3
- AbstractTrees 0.0.3
- ArrayViews 0.6.4
- AxisAlgorithms 0.1.5
- Benchmark 0.1.0
- BinDeps 0.4.2
- Blink 0.3.4
- Blosc 0.1.6
- BufferedStreams 0.1.6
- COFF 0.0.1
- CRC 1.1.1
- Calculus 0.1.15
- CodeTools 0.3.1
- Codecs 0.2.0
- ColorBrewer 0.3.0
- ColorTypes 0.2.5
- Combinatorics 0.3.2
- Conda 0.2.3
- Contour 0.1.1
- DWARF 0.0.3
- DataStructures 0.4.5
- DocStringExtensions 0.1.0
- Docile 0.5.23
- DualNumbers 0.2.2
- ELF 0.0.3
- FIONA 0.0.0- master (unregistered, dirty)
- FileIO 0.1.0
- FixedPointNumbers 0.1.4
- FixedSizeArrays 0.2.2
- ForwardDiff 0.2.2
- FunctionalCollections 0.1.3
- GZip 0.2.20
- GetC 1.1.1
- GtkUtilities 0.1.0
- Hexagons 0.0.4
- Hiccup 0.0.3
- Homebrew 0.3.4
- HttpCommon 0.2.6
- HttpParser 0.1.1
- HttpServer 0.1.6
- ImageJ 0.0.0- master (unregistered)
- IniFile 0.2.5
- Interpolations 0.3.5
- Iterators 0.1.10
- JuliaParser 0.7.4
- KernelDensity 0.2.0
- Kymograph 0.0.0- master (unregistered)
- LNR 0.0.2
- LaTeXStrings 0.2.0
- Lazy 0.11.0
- LegacyStrings 0.1.1
- Lexicon 0.1.18
- Libz 0.2.0
- Loess 0.0.7
- MachO 0.0.3
- MathProgBase 0.5.2
- MbedTLS 0.2.6
- Measures 0.0.3
- Media 0.2.1
- MicroManagerTIFFs 0.0.0- master (unregistered)
- Mux 0.2.1
- NaNMath 0.2.1
- Nettle 0.2.3
- NumericFuns 0.2.4
- ObjFileBase 0.0.3
- PDMats 0.4.2
- PimpMyREPL 0.0.0- master (unregistered)
- PlotUtils 0.0.4
- PositiveFactorizations 0.0.2
- Primes 0.1.1
- Ratios 0.0.4
- Reactive 0.3.4
- RecipesBase 0.0.6
- Reexport 0.0.3
- Registration 0.0.0- master (unregistered)
- Requests 0.3.9
- Requires 0.3.0
- Rmath 0.1.2
- RockTests 0.0.0- master (unregistered)
- Roots 0.2.1
- SHA 0.2.0
- ScikitLearnBase 0.1.1
- Showoff 0.0.7
- SortingAlgorithms 0.1.0
- Spots 0.0.0- master (unregistered)
- StatsFuns 0.3.0
- StructIO 0.0.2
- TerminalUI 0.0.2
- TexExtensions 0.0.3
- TextWrap 0.1.6
- TikzPictures 0.3.3
- Tokenize 0.0.0- master (unregistered)
- URIParser 0.1.6
- VT100 0.0.2
- WebSockets 0.2.0
- WoodburyMatrices 0.2.0
- ZipFile 0.2.6
- Zlib 0.1.12
staticfloat
commented
8 years ago If you run Pkg.build() does it happen as well?
rsrock
commented
8 years ago Yes, same thing with Pkg.build().
staticfloat
commented
8 years ago @rsrock I think I crushed this bug, turns out there was a new version of fontconfig available, but because we override it with our own, that newer version wasn't getting installed. I've updated our overriding version, so this should be all good to go now! After one last installation of fontconfig, you won't see this again. (Until, of course, a new version comes out, but at least then I'll know the symptoms and will be able to fix this faster)
rsrock
commented
8 years ago Sorry, doesn't seem to have fixed it for me. I even tried a Homebrew.rm("fontconfig"), and then I even tried deleting the bottle in my ~/Library/Caches/.... If I Pkg.build("Homebrew"), it still rebuilds fontconfig.
staticfloat
commented
8 years ago Please try running Pkg.checkout("Homebrew") to get the latest and greatest, then post the output of Pkg.build("Homebrew") again to make sure.
rsrock
commented
8 years ago Still have the same problem after checking out Homebrew master (I thought I had already done that, but I was wrong...). Here's the output:
julia> Pkg.build("Homebrew")
INFO: Building Homebrew
Already up-to-date.
Uninstalling fontconfig... (450 files, 2.9M)
==> Installing fontconfig from staticfloat/juliatranslated
==> Downloading https://homebrew.bintray.com/bottles/fontconfig-2.11.1_2.el_capitan.bottle.tar.gz
Already downloaded: /Users/rrock/Library/Caches/Homebrew.jl/fontconfig-2.11.1_2.el_capitan.bottle.tar.gz
==> Pouring fontconfig-2.11.1_2.el_capitan.bottle.tar.gz
==> Regenerating font cache, this may take a while
==> /Users/rrock/.julia/v0.5/Homebrew/deps/usr/Cellar/fontconfig/2.11.1_2/bin/fc-cache -frv
🍺 /Users/rrock/.julia/v0.5/Homebrew/deps/usr/Cellar/fontconfig/2.11.1_2: 450 files, 2.9M
Warning: Already linked: /Users/rrock/.julia/v0.5/Homebrew/deps/usr/Cellar/fontconfig/2.11.1_2The tarball that ends up in my Caches folder is from Feb 10, if that helps.
staticfloat
commented
8 years ago Huh. What is the output of using Homebrew; Homebrew.update()?
Homebrew should be trying to install fontconfig v2.12.1, not 2.11.1_2.
rsrock
commented
8 years ago julia> Homebrew.update()
Already up-to-date.
Uninstalling fontconfig... (450 files, 2.9M)
==> Installing fontconfig from staticfloat/juliatranslated
==> Downloading https://homebrew.bintray.com/bottles/fontconfig-2.11.1_2.el_capitan.bottle.tar.gz
Already downloaded: /Users/rrock/Library/Caches/Homebrew.jl/fontconfig-2.11.1_2.el_capitan.bottle.tar.gz
==> Pouring fontconfig-2.11.1_2.el_capitan.bottle.tar.gz
==> Regenerating font cache, this may take a while
==> /Users/rrock/.julia/v0.5/Homebrew/deps/usr/Cellar/fontconfig/2.11.1_2/bin/fc-cache -frv
🍺 /Users/rrock/.julia/v0.5/Homebrew/deps/usr/Cellar/fontconfig/2.11.1_2: 450 files, 2.9M
Warning: Already linked: /Users/rrock/.julia/v0.5/Homebrew/deps/usr/Cellar/fontconfig/2.11.1_2Here's something weird (and probably the source of the problem). If I look in ~/.julia/v0.5/Homebrew/deps/usr/Library/Taps/staticfloat/homebrew-juliadeps, I'm 15 commits behind (b71ab09). Nothing dirty in that dir.
tkelman
commented
8 years ago Wonder whether we're also susceptible to https://github.com/Homebrew/brew#update-bug ?
rsrock
commented
8 years ago Should I try that magic incantation?
staticfloat
commented
8 years ago Fascinating. Here's a Homebrew.jl-appropriate version:
using Homebrew
;cd $(Homebrew.brew_prefix)
;git fetch
;git reset --hard origin/master
;$(Homebrew.brew_exe) updateTry that and see if you're still seeing issues.
rsrock
commented
8 years ago Bingo! You've saved hours of my life. Thanks!
Lately, I've been getting this every time I update. The line about "this may take a while" is certainly true 😄
pinging @staticfloat