Following the instructions on http://plone.org/documentation/kb/how-to-upload-your-package-to-plone.org/distuttils-commands-and-.pypirc, I uploaded an egg to pypi (adi.workingcopyflag).The created egg is missing some files (configuration.zcml and profiles).
Why are these files missing/how can I fix this?
EDIT: Brandon Rhodes answer How to upload a pristine Python package to PyPI? helped.
Adding a MANIFEST.in is the solution.
I suggest you use zest.releaser to automatize the release process - less human mistakes:
http://opensourcehacker.com/2012/08/14/high-quality-automated-package-releases-for-python-with-zest-releaser/
For example, it would have warned you about missing MANIFEST.in.
(disclaimer: my blog post)
Related
I am currently working on a GitHub-based R package and I would like to add markdown text containing coding style guidelines. The problem is that I can't find the best place to put that information. According to Writing R Extensions, I can't just add a STYLE.md file without having the package fail basic build checks. They say:
The sources of an R package consists of a subdirectory containing a
files DESCRIPTION and NAMESPACE, and the subdirectories R, data, demo,
exec, inst, man, po, src, tests, tools and vignettes (some of which
can be missing, but which should not be empty). The package
subdirectory may also contain files INDEX, configure, cleanup,
LICENSE, LICENCE and NEWS. Other files such as INSTALL (for
non-standard installation instructions), README/README.md, or
ChangeLog will be ignored by R, but may be useful to end users.
So my current solution is to integrate the style guide into README.md file, but I don't like to have it there, because the guide is a secondary thing written for the package contributors and not the users; it should not be visible for everybody visiting the package's homepage (which is what happens for anything written in README.md and pushed to GitHub).
Another thing I thought about doing was to create a vignette for that; the developers of the rockchalk package did just that. However, my guide is much shorter, I don't think it fits well with the spotlight and printing-friendly format of vignettes.
Where else could/should I put the style guide?
I get this warning
Non-standard file/directory found at top level:
‘data-raw’
when building my package, even there is the recommendation of creating this folder to create package data http://r-pkgs.had.co.nz/data.html#data-sysdata
Any comments on that or do I need a specific setting to get rid of this message.
When used, data-raw should be added to .Rbuildignore. As explained in the Data section of Hadley's R-Packages book (also linked in the question)
Often, the data you include in data/ is a cleaned up version of raw data you’ve gathered from elsewhere. I highly recommend taking the time to include the code used to do this in the source version of your package. This will make it easy for you to update or reproduce your version of the data. I suggest that you put this code in data-raw/. You don’t need it in the bundled version of your package, so also add it to .Rbuildignore. Do all this in one step with:
usethis::use_data_raw()
I'm writing my first R package and have made a successful build with documentation using roxygen2 and added data sets.
However, I would also like ship an example script with how I use the functions in the r package. But I don't know where to put it.
Let's say I have created MyPackage. I have put my function scripts in the /R folder. Let's say I have:
foo1.R
foo2.R
foo3.R
Somewhere I'd also like to put a script with my workflow. Let's say I have a file, MyWorkflow.R:
library(MyPackage)
load(file='inData.R') # Loads indata variables A, B and C
X=foo1(A)
Y=foo2(X,B)
Z=foo3(Y,C)
Can I do this? If so, where do I put it? Is it an OK procedure - or generally frowned upon?
Any help or thoughts are appreciated.
Thanks.
Carl
Edit:
I looked at the link on demo/ and exec/, but didn't understand the exec/ folder thing. Grateful if you could clarify/exemplify/point to good uses of...
If I understand correctly, I'm not looking for an example or demo/, since the script won't necessarily be executable without tweaking by the user (e.g. to provide input data or paths). I "just" want to add an example script showing how I work with these functions.
I realise I should probably dive into the world of vignettes, but have difficulty in finding the time/oomph/energy to do so.
I also saw that there's the inst/ folder. Could you shed some light on the different uses of these options or hint at good examples of where they've been used (I often find examples more informative than reading an explanatory text that's above my level - I often get the feeling of being like a dog looking at a ceiling fan ;)
Will add info to the GitHub README. Thx for good suggestion!
Created inst/Workflow_Example/workflow.R. Upon build & reload, a Workflow_Example folder was created in the library with workflow.R script in it.
In combination with an explanatory remark in the README, this looks like what I was after. Problem solved or am I not seeing something obvious? Am I e.g. violating conventions/conduct/good practice?
You could either put it in demo/ or exec/ depending on the format of the script. See here for more details. I would mention the workflow and where it lives in the README regardless, and if you host your code on Github, you could create a wiki to describe the workflow and place the script there. This would be similar to what nrussell has mentioned in a comment above.
It is my first experience in writing an R-package. I used roxygen2 by following the instructions given in this link http://kbroman.org/pkg_primer/
Everythig is working fine except few things.. there could be a simpler solution to solve the issues, but I am not finding clues what I am doing wrong. I hope someone here in this blog can give a solution to solve my issues.
First issue is about {\code\link{function-name}} in roxygen2:
In .R script I inlcuded this line:
#' #seealso \code{\link{s2a}}
After documenting (generating .Rd files) there is no hyperlink to s2a ,
in documentation s2a shows like a normal text not like hyperlink..
export(s2a) is listed out in NAMESPACE.
Is there any other place i need to modify ?
Second issue is about data():
I saved the dataset in .Rdata format and placed in the data/ in package directory. I also created the .R script in R/ as like following steps here http://kbroman.org/pkg_primer/pages/data.html
In DESCRIPTION file LazyData: true .
but when I type data(shh) in R console gives a warning message
data(shh)
Warning message:
In data(shh) : data set ‘shh’ not found
Any ideas is of great help:)
It's been a while since you asked this, but I was having the exact same problem with hyperlinks in documentation not appearing correctly, so for anyone who might be having a similar problem: Are you possibly viewing the development documentation? The links don't seem to work there. (You'll know this is the case if you see Using development documentation for your_function_name in your console output when you run ?your_function_name.)
The links should appear in the non-development documentation. To generate this you can try building and reloading your package, for instance by following the steps here: http://r-pkgs.had.co.nz/man.html#man-workflow-2
I'm planning to condense some of my code into a package, and was looking at the source of a few published packages on CRAN as a guide. I notice many packages include the file R\zzz.R, so I presume there must be some convention surrounding this.
However, I cannot find any mention of zzz.R in the official Writing R Extensions guide. What is this file for, and do I need to include one in my package? Why is it named the way it is - why not zzzz.R?
It's a file where one usually puts actions on load of the package. It is tradition/convention that it's called zzz.R and could be called anything.R
You only need to include this if you want you package to do something out of the ordinary when it loads. Keep looking at what people put in there and you'll begin to get a sense of what they're used for.
This zzz.R file was also mentioned by Hadley Wickham in his book "R packages", at the bottom of "When you do need side-effects" section.
https://r-pkgs.org/Code.html#when-you-do-need-side-effects
If you use .onLoad(), consider using .onUnload() to clean up any side effects. By convention, .onLoad() and friends are usually saved in a file called R/zzz.R. (Note that .First.lib() and .Last.lib() are old versions of .onLoad() and .onUnload() and should no longer be used.)