Packager

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Voir bioconductor

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➤ Antoine commented:

J'ai réussi à créer un package contenant tout nos fichiers R (dans le dossier R) et fichiers Python (dans inst). Puis j'ai appris à faire les documentations de fonctions afin que help(mafonction) fonctionne après l'installation du package. En installant mon package, j'arrive bien à utiliser ma fonction Appel_Scriptv7 qui elle même appelle le fichier python. Les path relatifs semblent bien fonctionner car quand j'appelle ma fonction depuis la console de rstudio il me sort le bon résultat...

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➤ Ho Bich Hai commented:

ok cool. tu peux mettre le package dans github et permettre de l'installer par devtools?

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➤ Ho Bich Hai commented:

https://github.com/hadley/devtools

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➤ Antoine commented:

Oui j'ai tout fait avec devtools (créé le package, puis j'ai mis les fichiers R et python dedans). Puis pour l'installer j'ai juste fait devtools::install("monPackage")

Donc oui on peut l'installer avec devtools. OK je le mettrai demain sur github, je verrai avec Julien ou le mettre....

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➤ Antoine commented:

Hai, j'ai vérifié et quand je fais devtools::install("RRicePackage") le package s'installe parfaitement bien, j'ai bien accès à la documentation et je peux bien appeler les fonctions grâce au package. Je vais commencer ma tâche pour la fonction Calldb1 et je continuerai à mettre à jour à chaque fois la documentation de chaque fonction.

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➤ Ho Bich Hai commented:

ok just tell me when you sync with Julien to have that on github so that I can test. The name of the package is changed to rRice.

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➤ Ho Bich Hai commented:

I can't use devtools::install("rRice") to install this package yet?

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➤ Ho Bich Hai commented:

Antoine next thing to after fixing this devtools is to learn r-hub. This is used to build and maintain R packages with good practices

https://github.com/r-hub/proposal https://github.com/r-hub/rhub

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➤ Ho Bich Hai commented:

also with Bioconductor, the repos we will deposit our package. Please check if they have specific requirement.

Antoine please write a document on packaging and maintaining R packages with good practices based on Wickham's guide, r-hub and bioconductor (for our case). This is a part of your final report.

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➤ Ho Bich Hai commented:

Julien please follow this, especially r-hub for R builder. We need to have the package checked with r-hub.

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➤ Antoine commented:

Thé document that I have to write will explain how tout use thé package ans how to install it on a computer ?

Okay i'll check tomorrow for thé problem with devtools.

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➤ Ho Bich Hai commented:

Yes it is user guide. But I need a document to explain how an R package is built, tested and maintained by good practices based on Wickham's guide, r-hub and bioconductor. It is a note of what you are doing regarding packaging.

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➤ Antoine commented:

Thé structure of thé document is made with 4 big parts : the basics of R package (everything important will be in this part), the organization of rRice structure, the coding style with bioconductor, r-hub.

Do you think the structure is good or do you want something totally different ? Yesterday i have worked on the structure of rRice and bioconductor and today i'm working on the basics of R package (with explanation of how works DESCRIPTION file, how is made à package, and how to release à package,....)

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➤ Ho Bich Hai commented:

r-hub is for testing the pacakge so it should be in the first part.

1. R packaging and testing
2. Bioconductor style and submission test/procedure
3. rRice

would be good. You can start the document in googledocs and keep it in Internship folder. Pls notify me when you want me to have a look.

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➤ Antoine commented:

I'm writing it in gedit (txt document) because it's easier for me but when i will finish, i'll put everything in à Google Doc and i'll organize it. Today I only work on Reste packaging and i'm going tout finish this part tomorrow and i'll start r-hub

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➤ Ho Bich Hai commented:

No, you need to write document in a way that I follow, not in your own machine til you finish. You can keep notes etc. to yourself the way you like but for a collaborative work, use either googledocs or better Rmarkdown.

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➤ Antoine commented:

Okay no problems hai, I will put everything I have done in Google Doc or Rmarkdown

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➤ Antoine commented:

I had few problems with r markdown. So, i decided to create a Google docs that you will be able to get on rRice drive to shared with me. The name of the document is "UserGuide" if you want to have a look.

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➤ Ho Bich Hai commented:

OK but this is not a user guide. This is your research on R packaging and testing, hence your report. Users don't need to see this at all. Please continue and tell me once you need me to check.

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➤ Antoine commented:

Oh yeah, i'm gonna change the name of the document then. Hai, what do think about the document ? Do you want more details in the explanations or it is good ?