devtools::check() / R CMD check - Githubissues

boettiger-lab / despot

:package: wrapper for the DESPOT algorithm for solving online POMDP problems

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devtools::check() / R CMD check #10

Open cboettig opened 7 years ago

cboettig commented 7 years ago

@glimow

Hi Tristan,

Despot is looking good! When you get a chance, try running devtools::check() in R from the package root directory to both run the unit tests and get a list of a few odds and ends that can be cleaned up in the package.

glimow commented 7 years ago

Yup, on my computer devtools::check() pass all the tests, there is only a few compilation warning which I should fix soon. Haven't tested on mac however.

glimow commented 7 years ago

@cboettig Hi Carl, Despot passes all tests and checks without errors. I also fixed all warnings but one, which I can't get rid off. devtools::check() is telling me Source packages should not contain undeclared executable files. I tried to put the executable path in a BinaryFiles file, as it is said in the R package doc. but it does not work. Apart from that, everything should work fine.

cboettig commented 7 years ago

Great, thanks, I'll take a look. Ideally there should be no warnings and as few Notes as possible (Notes are okay but have to be explained whenever we submit to CRAN).

Maybe a stupid question: Why is inst/bin/pompdx executable included in the sources? Can't this be built from the source-code?

glimow commented 7 years ago

In fact it is. Probably a mistake of mine, perhaps the makefile is erasing the old executable before compiling it again and that's why I did not find the issue. I am looking at it, Thanks Also, there is 4 Notes for now.

cboettig commented 7 years ago

Great. I think it would also be a good time to toggle this repo over to public so we connect the travis-ci.org integration for checks etc. Sound good?

glimow commented 7 years ago

Sounds good, I do not have experience with connecting the travis-ci.org checks but I will look at it. Also, for the Readme, I just put an "?" for the OSX version because I do not know which one you and/or milad are using. Feel free to correct it if the package works fine on your system

cboettig commented 7 years ago

devtools::use_travis() should get you going pretty quickly. Also see https://docs.travis-ci.com/user/languages/r/ .

glimow commented 7 years ago

Okay, sounds that there is no need to have experience. May you just make the repo public so I can test please ?

cboettig commented 7 years ago

yup, repo is now public :-)

glimow commented 7 years ago

oh, okay travis say that it cannot access the repo boettiger-lab/despot. I am looking at it, certainly a missed conf somewhere EDIT: On the travis website, it says that I cannot allow travis to look at despot because I am not admin of this repo, do you needed that to test before ? Or should calling travis from the console work just fine ?

cboettig commented 7 years ago

@glimow Ah, good catch. Just made you an admin.

glimow commented 7 years ago

@cboettig package successfully installs itself into travis CI test env !

cboettig commented 7 years ago

Nice!

Can you add the markdown badge to the README? (You'll see these badges pretty often on GitHub source code; they provide a quick way to see / indicate if the most recent builds are woking).

Also would be good to enable the code coverage check on travis, see the function devtools::use_coverage() function to get started. You may need to toggle codecov.io on in the same way you did for travis.
The last one of these to add is probably devtools::use_appveyor(), which will test that the package installs on Windows. (but no worries if you haven't figured out the windows install.)

glimow commented 7 years ago

A bit of news between two python functions :

Markdown badge added to the Readme
devtools::use_appveyor() returns an error, on the appveyor website the console is telling that Project file "despot.Rproj" is not a valid MSBuild project file which must be an XML. which is strange because the .rproj file is generated by RStudio, so I am surprised it is source of problems.
devtools::use_coverage() is on it's way ! I am doing a little config about it right now

cboettig commented 7 years ago

You don't seem to have a .Rbuildignore file committed -- devtools should create this file and automatically be adding files like *.Rproj to this list, since though they are used by RStudio and other services, they are not part of the official R package spec

glimow commented 7 years ago

Okay,.Rbuildignore file commited but still same error from appveyor. Strange because the file is in the .Rbuildignore. I continue checking