Errors while trying to use JuMP

[Kostas Tavlaridis-Gyparakis]

Hello,
I am really new to Julia and not the best programmer mysefl.
I run linux mint 16 and I installed julia via terminal (sudo apt-get install julia ).
Then when I run Julia on my terminal, while the JuMP package is installed
sth that I believe the following two commands on my terminal prove:

julia> Pkg.update()
INFO: Updating METADATA...
INFO: Computing changes...
INFO: No packages to install, update or remove

julia> Pkg.add("JuMP")
INFO: Nothing to be done

Then when I try to use JuMP I get the following error msg:

julia> using JuMP
ERROR: Block not defined
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in reload_path at loading.jl:152
in _require at loading.jl:67
in require at loading.jl:54
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in reload_path at loading.jl:152
in _require at loading.jl:67
in require at loading.jl:54
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in reload_path at loading.jl:152
in _require at loading.jl:67
in require at loading.jl:54
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in reload_path at loading.jl:152
in _require at loading.jl:67
in require at loading.jl:54
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in reload_path at loading.jl:152
in _require at loading.jl:67
in require at loading.jl:51
while loading /home/kostas/.julia/v0.3/Docile/src/types.jl, in expression starting on line 2
while loading /home/kostas/.julia/v0.3/Docile/src/Docile.jl, in expression starting on line 19
while loading /home/kostas/.julia/v0.3/DataStructures/src/DataStructures.jl, in expression starting on line 48
while loading /home/kostas/.julia/v0.3/Graphs/src/Graphs.jl, in expression starting on line 2
while loading /home/kostas/.julia/v0.3/ReverseDiffSparse/src/coloring.jl, in expression starting on line 1
while loading /home/kostas/.julia/v0.3/ReverseDiffSparse/src/ReverseDiffSparse.jl, in expression starting on line 20
while loading /home/kostas/.julia/v0.3/JuMP/src/JuMP.jl, in expression starting on line 13

Finally the msg I receive for Block is the following:

julia> Pkg.checkout("Block")
ERROR: Block is not a git repo
in checkout at pkg/entry.jl:190
in anonymous at pkg/dir.jl:28
in cd at ./file.jl:20
in cd at pkg/dir.jl:28
in checkout at pkg.jl:33

[Joey Huchette]

What’s the output of Pkg.status()? It seems like an issue with Docile, not JuMP.

[Kostas Tavlaridis-Gyparakis]

Here is the output I get:

julia> Pkg.status()
4 required packages:
 - CPLEX                         0.0.9
 - Images                        0.4.37
 - Jewel                         1.0.4
 - JuMP                          0.5.8
27 additional packages:
 - AnsiColor                     0.0.2
 - BinDeps                       0.3.9
 - Calculus                      0.1.4
 - Color                         0.4.5
 - Compat                        0.4.4
 - Compose                       0.3.12
 - DataStructures                0.3.9
 - Docile                        0.1.0
 - DualNumbers                   0.1.0
 - FactCheck                     0.1.2
 - FixedPointNumbers             0.0.7
 - Graphics                      0.1.0
 - Graphs                        0.4.3
 - Iterators                     0.1.7
 - JSON                          0.4.0
 - JuliaParser                   0.6.2
 - LNR                           0.0.1
 - Lazy                          0.8.4
 - Markdown                      0.3.0
 - MathProgBase                  0.3.1
 - Requires                      0.1.2
 - ReverseDiffSparse             0.1.2
 - SHA                           0.0.4
 - SIUnits                       0.0.3
 - TexExtensions                 0.0.2
 - URIParser                     0.0.5
 - Zlib                          0.1.8

[Kostas Tavlaridis-Gyparakis]

Pkg.add("Docile")

INFO: Nothing to be done

INFO: METADATA is out-of-date — you may not have the latest version of Docile
INFO: Use `Pkg.update()` to get the latest versions of your packages

[Seth]

Might not be related, but your Docile package is way out of date. It's currently at 0.5.6, and you appear to be running 0.1.0.

On Saturday, June 13, 2015 at 3:36:39 AM UTC-5, Kostas Tavlaridis-Gyparakis wrote:

Pkg.add("Docile")
INFO: Nothing to be done
INFO: METADATA is out-of-date — you may not have the latest version of Docile
INFO: Use `Pkg.update()` to get the latest versions of your packages

 - Docile                        0.1.0

[Kostas Tavlaridis-Gyparakis]

Only problem is that when I run the updtate command in julia I receive a msg that there is nothing to be upgraded:

Pkg.update()
INFO: Updating METADATA...
INFO: Computing changes...
INFO: No packages to install, update or remove

[SVAKSHA]

On Sat, Jun 13, 2015 at 9:44 AM, Kostas Tavlaridis-Gyparakis
<kostas.t...@gmail.com> wrote:
> Only problem is that when I run the updtate command in julia I receive a msg
> that there is nothing to be upgraded:

Try the update command after you manually delete the "Docile" package
from `~/.julia/.cache` and `v0.4/` folders. <-- Do check the julia
version your system has. Before doing this take a backup of the
`.julia` folder, just in case...

HTH,
SVAKSHA ॥ http://about.me/svaksha ॥

[SVAKSHA]

On Sat, Jun 13, 2015 at 9:57 AM, SVAKSHA <sva...@gmail.com> wrote:
> On Sat, Jun 13, 2015 at 9:44 AM, Kostas Tavlaridis-Gyparakis
> <kostas.t...@gmail.com> wrote:
>> Only problem is that when I run the updtate command in julia I receive a msg
>> that there is nothing to be upgraded:
>
> Try the update command after you manually delete the "Docile" package

After you delete Docile, try Pkg.add("Docile"), then Pkg.update()

[Kostas Tavlaridis-Gyparakis]

Followed your recommendation but have to note the following things:

1) I have Julia v0.3 even if I just downloaded Julia this week
2) after deleting Dolice and running update command again the version 0.1 was installed:

Pkg.update()
INFO: Updating METADATA...
INFO: Computing changes...

INFO: Cloning cache of Docile from git://github.com/MichaelHatherly/Docile.jl.git
INFO: Installing Docile v0.1.0

[Kostas Tavlaridis-Gyparakis]

Also, if I try to update Dolice (after having deleting it from the above mentioned directories)
 by first typing Pkg.add("Dolice") I receive following error:

Pkg.add("Docile")
ERROR: unknown package Docile
 in wait at task.jl:51
 in sync_end at ./task.jl:306
 in add at pkg/entry.jl:314
 in add at pkg/entry.jl:71

 in anonymous at pkg/dir.jl:28
 in cd at ./file.jl:20

 in __cd#226__ at ./pkg/dir.jl:28
 in add at pkg.jl:20


I can only install it if I directly run the Pkg.update() command, which does install v. 0.1 as mentioned above

[SVAKSHA]

On Sat, Jun 13, 2015 at 10:03 AM, Kostas Tavlaridis-Gyparakis
<kostas.t...@gmail.com> wrote:
> Followed your recommendation but have to note the following things:
>
> 1) I have Julia v0.3 even if I just downloaded Julia this week
> 2) after deleting Dolice and running update command again the version 0.1
> was installed:

Run update after installing Docile. I'm on 0.4 so I dont know what
version of Docile the stable version installs, but try using
`Pkg.pin()` to force a specific version of the package. Unregistered
packages can be installed via the url, so you can try
Pkg.clone("git://example.com/path/to/Package.jl.git")
SVAKSHA ॥ http://about.me/svaksha ॥

[Kostas Tavlaridis-Gyparakis]

When i run update after I install Dolice there is nothing new:

Pkg.update()
INFO: Updating METADATA...
INFO: Computing changes...

INFO: No packages to install, update or remove

How can I update from terminal to julia 0.4 myself?
Also I am not quiet sure how to use clone command
to force julia Dolice to the latest version (sorry I am
a real noob).

[Tim Holy]

Check to see what Pkg.status() says. You may have another package that is
pinning Docile at 0.1?

--Tim

[Kostas Tavlaridis-Gyparakis]

Here is the outcome of Pkg.status():

Pkg.status()
5 required packages:
 - CPLEX                         0.0.9
 - Docile                        0.1.0

 - Images                        0.4.37
 - Jewel                         1.0.4
 - JuMP                          0.5.8

26 additional packages:

 - AnsiColor                     0.0.2
 - BinDeps                       0.3.9
 - Calculus                      0.1.4
 - Color                         0.4.5
 - Compat                        0.4.4
 - Compose                       0.3.12
 - DataStructures                0.3.9

 - DualNumbers                   0.1.0
 - FactCheck                     0.1.2
 - FixedPointNumbers             0.0.7
 - Graphics                      0.1.0
 - Graphs                        0.4.3
 - Iterators                     0.1.7
 - JSON                          0.4.0
 - JuliaParser                   0.6.2
 - LNR                           0.0.1
 - Lazy                          0.8.4
 - Markdown                      0.3.0
 - MathProgBase                  0.3.1
 - Requires                      0.1.2
 - ReverseDiffSparse             0.1.2
 - SHA                           0.0.4
 - SIUnits                       0.0.3
 - TexExtensions                 0.0.2
 - URIParser                     0.0.5
 - Zlib                          0.1.8

[Miles Lubin]

What is the output of versioninfo() (at the Julia command line)?

Also, try deleting your ~/.julia directory and reinstalling the packages you need.

[Kostas Tavlaridis-Gyparakis]

The output of versioninfo() is the following:

Julia Version 0.3.0-rc1+54
Commit 4e92487 (2014-07-17 05:40 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i5-4300U CPU @ 1.90GHz
  WORD_SIZE: 64
  BLAS: libblas.so.3
  LAPACK: liblapack.so.3
  LIBM: libopenlibm


I already deleted the Docile package from the julia directory and reinstalled it,
but again with no luck and also again the old version of 0.1 was installed.

[Miles Lubin]

You're using a prerelease version of 0.3 from nearly a year ago. Not sure how this came to be installed, but you'll need to update to 0.3.0 release or later.

[Kostas Tavlaridis-Gyparakis]

Ok, so after deleting all the julia files from my laptop
and downloading the latest version from github (

git clone git://github.com/JuliaLang/julia.git

), when I try to run make in the terminal after a huge run of 50 minutes
in the end the following msg is desplayed in my terminal:

checking for suitable m4... configure: error: No usable m4 in $PATH or /usr/5bin (see config.log for reasons).
make[1]: *** [gmp-6.0.0/config.status] Error 1
make: *** [julia-deps] Error 2

[Kostas Tavlaridis-Gyparakis]

Ok fixed that one, but now I have another installation problem,
I receive the following error:
/bin/sh: 2: cmake: not found
make[1]: *** [libgit2/build/Makefile] Error 127

make: *** [julia-deps] Error 2

Once I do finally manage to sucessfully install julia I will come back to you!

[Tony Kelman]

Check the list of required built tools here https://github.com/JuliaLang/julia#required-build-tools-and-external-libraries if you want to build from source. Note that unless you're contributing to Julia development, you should build from the release-0.3 stable branch.

You shouldn't have to build from source though, have you tried the generic Linux binaries from http://julialang.org/downloads/ ? Download and extract https://julialang.s3.amazonaws.com/bin/linux/x64/0.3/julia-0.3.9-linux-x86_64.tar.gz and it should work right away.

[Kostas Tavlaridis-Gyparakis]

I downloaded and extracted the version that you put in the link, but for some reason now, when I run
Julia on terminal the pck command doesn't seem to work.
This is the msg I get when I try to use any command related with pkd:

Pkg.status()
ERROR: could not spawn `git version`: no such file or directory (ENOENT)
 in _jl_spawn at process.jl:217
 in spawn at process.jl:348
 in open at ./process.jl:397
 in readbytes at ./process.jl:461
 in version at ./pkg/git.jl:34
 in init at ./pkg/dir.jl:32
 in cd at pkg/dir.jl:25
 in status at pkg.jl:28 (repeats 2 times)

[Tony Kelman]

Which Linux distribution are you using? That error most likely means you don't have git installed, you need to manually install it through your distribution's package manager (apt-get, yum, pacman, zypper, etc). I'm a little surprised Pkg commands were able to work from the 0.3-prerelease version of Julia that you had been using (where did that come from anyway?). I think there was a git version check added in to the initialization of Pkg since the previous version you had been using.

[Kostas Tavlaridis-Gyparakis]

The 0.3-prerelease version of Julia was installed in my machine when I tried to isntall julia from the terminal
by typing "sudo apt-get install julia".
I run linux mint 16 on my laptop.
When I try to apt-get install git, I receive the following error:

Traceback (most recent call last):
  File "/usr/lib/command-not-found", line 21, in <module>
    os.execvp("python3", [sys.argv[0]] + sys.argv)
  File "/usr/lib/python2.7/os.py", line 344, in execvp
    _execvpe(file, args)
  File "/usr/lib/python2.7/os.py", line 380, in _execvpe
    func(fullname, *argrest)
OSError: [Errno 2] No such file or directory

[Tony Kelman]

I see. I'm a little surprised a distribution chose to package a prerelease (but then again there was only one bugfix release between 0.2 and 0.3, so maybe not).

I have no idea why installing git would try to do execvp on python3, but that looks like you need to install python3?

According to http://www.linuxmint.com/oldreleases.php, Linux Mint 16 has been "Obsolete since July 2014" so you may also need to upgrade to a supported version of the distribution for the package manager to work properly. I'm not sure.

[Kostas Tavlaridis-Gyparakis]

Ok, I'll proceed with the upgrades tomorrow and let you know.
Thanks a lot for all the help so far hope tomorrow I will finally have
JuMP working.

[Kostas Tavlaridis-Gyparakis]

So finally after upgrading my OS (actually switched to Ubuntu),
JuMP finally works!
Thanks a lot for all the help, probably I will come back with other questions regarding
connecting C++ code with Julia in the future, but for the moment problem solved!