Julia - how to update WinRPM in julia version 0.6.4 - julia

I'm new to Julia and I want to use COBRA Package.
For adding COBRA I use command :
Pkg.add("COBRA")
But when running, I get these errors:
INFO: Building WinRPM
WARNING: skipping repodata/repomd.xml, not in cache -- call WinRPM.update() to download
WARNING: skipping repodata/repomd.xml, not in cache -- call WinRPM.update() to download
INFO: Downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
WARNING: Unknown download failure, error code: 2148270086
WARNING: Retry 1/5 downloading: https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
until:
WARNING: Unknown download failure, error code: 2148270086
WARNING: Retry 5/5 downloading: https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
WARNING: received error 0 while downloading
https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_42.2/repodata/repomd.xml
After these errors, I have checked the link and I've found out the source is not there, anymore.
So then I ran this command as said above:
WinRPM.update()
But it has thrown this error:
ERROR: UndefVarError: WinRPM not defined
Please Help me to add COBRA to Julia. I'm using version 0.6.4 because Cobra does not work on the next versions.(Windows 10)
Any help would be appreciated.

The problem, as you've mentioned, is that the original sources used by the package aren't valid URLs anymore. The proper way to solve this is to open a pull request with the package to change the URLs (which I've now done here ). As a stopgap measure, here's a hacky way to work around this issue for now:
Do a Pkg.add("WinRPM"). This might trigger the same warnings as above, ignore these.
Next, using WinRPM to load the package we added
Now, the source URLs are read from the sources.list file (linked above) into a global WinRPM.sources variable. We're going to edit this variable's contents to point to new working URLs. (This is generally a terrible idea, to directly poke into the internals of a module and change things.)
julia> WinRPM.sources[:] = replace.(WinRPM.sources, "Leap_42.3" => "Leap_15.3")
2-element Vector{String}:
"https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_Leap_15.3"
"https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win64/openSUSE_Leap_15.3"
A WinRPM.update() should now work, and download things into a local cache.
I'm using version 0.6.4 because Cobra does not work on the next versions.
I hope you mean Julia 1.6.4 here, or version 0.6.4 of something else in the stack. If you mean Julia version 0.6.4, you might face further problems down the road and find it hard to get support for such an old version.

Related

Circularity detected when running (vega:load-vega-examples)

When I load the vega-lite data sets using
(vega:load-vega-examples)
I get the following error:
Could not REQUIRE CL-DATE-TIME-PARSER: circularity detected. Please check your configuration
However, the examples appear to have loaded.
Also, before I installed cl-date-time-parser in quicklisp, I was getting an error message similar to:
Do not know how to REQUIRE CL-DATE-TIME-PARSER
Does anyone know how to get rid of these errors?
Many thanks!
The IMDB example requires cl-date-time-parser. I suspect that problem is that (require ...) only works when the library is in a location known to ASDF. In a new installation, this may not be the case. Now reported as issue #19.
Try loading the library with quicklisp and then rerunning load-vega-examples.

nbsphinx causes build to fail when building Jupyter Notebooks

Details
I am getting a build failure of my read-the-docs that I don't understand. The assertion of "verbatim" in line 2151 of nbsphinx.py is causing the build failure. So the build fails when I try to include the Jupyter Notebook tutorials I created. I compared current versions of the tutorials to previous versions which had not caused the build to fail, and I can't find a difference that could account for the current failure.
Read the Docs project URL: lofti_gaia
Build URL: https://github.com/logan-pearce/lofti_gaia
Read the Docs username: logan-pearce
Expected Result
A passing build including *.ipynb files
Actual Result
Build failed at line 2151 of nbsphinx.py due to assertion of 'Verbatim' failing.
Terminal output:
Running Sphinx v4.1.2
loading translations [en]... done
making output directory... done
WARNING: html_static_path entry '_static' does not exist
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
processing lofti_gaia.tex... index installation tutorials/QuickStart tutorials/Tutorial api lofti loftitools
resolving references...
done
writing... failed
Exception occurred:
File "/home/docs/checkouts/readthedocs.org/user_builds/lofti-gaia/conda/latest/lib/python3.7/site-packages/nbsphinx.py", line 2151, in depart_codearea_latex
assert 'Verbatim' in lines[0]
AssertionError
The full traceback has been saved in /tmp/sphinx-err-x1h83s3m.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
According to the github issue 584 for nbsphinx (https://github.com/spatialaudio/nbsphinx/issues/584), this is due to a compatibility issue with sphinx 4.1.0. It can be gotten around by requiring sphinx version 4.0.2.
So in my requirements.txt file, I included sphinx==4.0.2, after which the build passes. So now my requirements.txt file looks like:
numpy
matplotlib
astropy>=4.0.1.post1
astroquery>=0.4
sphinx==4.0.2
ipython==7.19.0
nbsphinx>=0.8.6
and the build passes.
I have encountered the same issue. I did not solve it with .ipynb format, but converting the jupyter notebook to .rst format works.
May it helps

Workaround to allow badges in package README.md on github but not in CRAN version

R CMD check packagename_0.1.1.tar.gz --as-cran produces a WARNING if badges are present in README.md. This causes consequences like travis CI to fail (since it treats warnings as errors)
Is there a workaround to get the check to pass without removing the badges?
Here is an example of the WARNING I see
* checking top-level files ... WARNING
Conversion of ‘README.md’ failed:
pandoc: Could not fetch https://www.r-pkg.org/badges/version/bigrquery
TlsExceptionHostPort (HandshakeFailed (Error_Misc "user error (unexpected type received. expecting handshake and got: Alert [(AlertLevel_Fatal,HandshakeFailure)])")) "www.r-pkg.org" 443
Related: pandoc: Could not fetch http://www.r-pkg.org/badges/version/package TlsExceptionHostPort (HandshakeFailed
This is a workaround to embed (static) badges in pages. They do not auto-update. The purpose is to avoid offline derived errors.
Take a look at readme files in:
https://gitlab.com/ferroao/idiogramFISH. This also handles errors while installing with devtools in windows, a process that does not have online connectivity (see vignette index.Rmd). Look at DESCRIPTION also if you want to see dependencies and vignette builders.
Generate the .md from the .Rmd (Rmarkdown).
Months on, I discovered the problem. When I installed anaconda, it changed the version of pandoc my system used - which pandoc should return something like /usr/local/bin/pandoc (and not like /Users/st/anaconda3/bin/pandoc).
In my case, I edited by .bash_profile to exclude ananconda, closed and reopened the terminal and everything worked. (I also reinstalled pandoc from here, but I don't think that had anything to do with fixing it - it did show me the default installation location though)

Weird issue while testing R package: package `[package name]` found more than once, using the first from [file path]

I'm working on a somewhat complex package (that I unfortunately can't share) that involves a Shiny app, and it an issue has surfaced where I'm getting these warnings when testing:
package [package name] found more than once, using the first from [file path]
In library(testthat) : package ‘testthat’ already present in search()
The first one occurs because I'm using system.file to pull a file in inst that I use for testing.
I've tried to do some debugging with .libPaths and by forcing system.file to go to the .libPaths default with the lib.loc argument, but that doesn't do anything.
I've tried uninstalling the package, which works because then there are not multiple results for find.package.
It seems like testthat adds the current directory to the library paths while it's running, and this creates the issue with system.file and consequently, find.package.
I'm really confused as to what's causing this. I'm combing through the changes I've made and I can't seem to find anything. Any ideas are helpful. I've tried googling this error messages and all that comes up is the source.
The issue here was with changing the option setting for verbose. That caused more output to result from the code, which broke a lot of tests. I hope this helps someone in the future.

Julia error: no method haskey(Dict{String,Dict{String,String}},ASCIIString)

I'm trying to test out the Winston plotting engine in Julia. I installed the package but I'm getting some errors now when I try to compile one of the examples:
> julia example1.jl
Warning: could not import Base.haskey into Inifile
Warning: could not import Graphics.set_source into Color
ERROR: no method haskey(Dict{String,Dict{String,String}},ASCIIString)
in read at /Users/thinkpad20/.julia/IniFile/src/IniFile.jl:41
in read at /Users/thinkpad20/.julia/IniFile/src/IniFile.jl:67
in anonymous at /Users/thinkpad20/.julia/Winston/src/Winston.jl:39
in include_from_node1 at loading.jl:88
in reload_path at loading.jl:111
in require at loading.jl:46
in include_from_node1 at loading.jl:88
in process_options at client.jl:253
in _start at client.jl:334
at /Users/thinkpad20/.julia/Winston/src/Winston.jl:31
at /Users/thinkpad20/.julia/Winston/examples/example1.jl:3
can anyone tell me what's going on? It seems to be that it can't find Base.haskey, but I'm not sure how to address that.
Try inspecting Base.VERSION
haskey was introduced in Julia v0.2 (still pre-release as of this writing), I suspect that you are running a version 0.1.x
The real problem is inside of the Winston package. It sounds like they have their REQUIRES information set up wrong. You should file an issue here: https://github.com/nolta/Winston.jl
You can also download pre-release version of 0.2 for windows and mac here: https://code.google.com/p/julialang/downloads/list

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