MbedTLS package is "dirty"

[yordiak]

Here is the output of Pkg.status() command

5 required packages:
 - Atom                          0.5.7
 - DataFrames                    0.8.5
 - DecisionTree                  0.5.1
 - Distributions                 0.11.1
 - IJulia                        1.3.2
 - MbedTLS                       0.3.0              18dfb5cd (dirty)
 - Plots                         0.10.2
 - QuantEcon                     0.8.0
 - Stats                         0.1.0
 - StatsBase                     0.11.1
 - StatsFuns                     0.3.1
 - StochDynamicProgramming       0.2.2
 - StochasticDiffEq              0.3.0
 - Stochy                        0.0.2
 - Symata                        0.2.0
90 additional packages:
 - ASTInterpreter                0.0.4
 - AbstractTrees                 0.0.4
 - ArgParse                      0.4.0
 - AutoHashEquals                0.0.10
 - AxisAlgorithms                0.1.5
 - BinDeps                       0.4.5
 - Blink                         0.5.0
 - Blosc                         0.1.7
 - COFF                          0.0.2
 - CRC                           1.2.0
 - Calculus                      0.1.15
 - ChunkedArrays                 0.1.1
 - CodeTools                     0.4.3
 - Codecs                        0.2.0
 - ColorTypes                    0.2.12
 - Colors                        0.6.9
 - Combinatorics                 0.3.2
 - Compat                        0.9.5
 - Conda                         0.4.0
 - DSP                           0.1.1
 - DWARF                         0.1.0
 - DataArrays                    0.3.10
 - DataStructures                0.4.6
 - DiffEqBase                    0.3.2
 - ELF                           0.1.0
 - EllipsisNotation              0.0.2
 - FileIO                        0.2.0
 - FixedPointNumbers             0.2.1
 - FixedSizeArrays               0.2.5
 - ForwardDiff                   0.2.5
 - GZip                          0.2.20
 - Gallium                       0.0.4
 - HDF5                          0.7.0
 - Hiccup                        0.1.1
 - HttpCommon                    0.2.6
 - HttpParser                    0.2.0
 - HttpServer                    0.1.7
 - Interpolations                0.3.6
 - Iterators                     0.2.0
 - JLD                           0.6.7
 - JSON                          0.8.0
 - JuMP                          0.14.2
 - JuliaParser                   0.7.4
 - Juno                          0.2.5
 - LNR                           0.0.2
 - Lazy                          0.11.4
 - LegacyStrings                 0.1.1
 - LightGraphs                   0.7.2
 - LightXML                      0.4.0
 - MachO                         0.0.4
 - MacroTools                    0.3.4
 - MathProgBase                  0.5.8
 - Measures                      0.0.3
 - Media                         0.2.4
 - Mustache                      0.1.2
 - Mux                           0.2.2
 - NaNMath                       0.2.2
 - Nettle                        0.2.4
 - ObjFileBase                   0.0.4
 - PDMats                        0.5.2
 - Parameters                    0.5.0
 - ParserCombinator              1.7.11
 - PlotThemes                    0.1.0
 - PlotUtils                     0.2.0
 - Polynomials                   0.1.1
 - Primes                        0.1.1
 - ProgressMeter                 0.3.3
 - PyCall                        1.7.2
 - Ranges                        0.0.1
 - Ratios                        0.0.4
 - Reactive                      0.3.6
 - RecipesBase                   0.1.0
 - RecursiveArrayTools           0.1.1
 - Reexport                      0.0.3
 - ResettableStacks              0.0.1
 - ReverseDiffSparse             0.5.8
 - Rmath                         0.1.5
 - SHA                           0.3.0
 - ScikitLearnBase               0.2.1
 - Showoff                       0.0.7
 - SimpleTraits                  0.2.0
 - SortingAlgorithms             0.1.0
 - StructIO                      0.0.2
 - TerminalUI                    0.0.2
 - TextWrap                      0.1.6
 - URIParser                     0.1.6
 - VT100                         0.0.2
 - WebSockets                    0.2.1
 - WoodburyMatrices              0.2.1
 - ZMQ                           0.4.0

I tried Pkg.rm and Pkg.build commands but they don't work.

How to "clean" MbedTLS?

I am running julia on a manjaro linux 64-bit system

[quinnj]

What version of Julia are you using? Not sure why things are getting marked as dirty, particularly on that old of a version (0.3.0 was tagged in august). A couple of "manual" options you have are:

• Navigate to your ~/.julia/v0.4/MbedTLS or ~/.julia/v0.5/MbedTLS and then do git status to see what's dirty, you can then do a git checkout [file] to reset it to normal state.
• You could also navigate to ~/.julia/v0.4 and just delete the entire MbedTLS directory, then from julia, do Pkg.add("MbedTLS") again.

If you wouldn't mind trying the first option and reporting back the offending file, we'd appreciate knowing what happened in case it's something that can still happen on master.

[mlubin]

JuliaLang/julia#7054

[yordiak]

I am using Julia v0.5

Here is the output of git status command

Not currently on any branch.
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   deps/cmake_check.sh

If I go to deps subfolder and then type git checkout cmake_check.sh, then I get

error: pathspec 'cmake_ckeck.sh' did not match any file(s) known to git.

Since I am new to the Linux community, I don't know how to solve the problem

[tkelman]

'cmake_ckeck.sh' did not match any file(s) known to git

means you misspelled that

[tkelman]

As with #91, the underlying issue is JuliaLang/julia#17610 - there is a bug in either the Julia libgit2 bindings or the libgit2 C library, or how we're calling them in Pkg, that is not handling executable permissions correctly. Needs someone to dig into the bindings and track down where it's happening, since the author of the Julia libgit2 bindings and Pkg rewrite has vanished.

[samoconnor]

@quinnj obsolete issue? should be closed?