From jori@mey@ @ending from gm@il@com  Thu Dec  6 18:40:10 2018
From: jori@mey@ @ending from gm@il@com (Joris Meys)
Date: Thu, 6 Dec 2018 18:40:10 +0100
Subject: [Rd] Dealing with .git folder when using R CMD INSTALL
In-Reply-To: <23561.15485.544650.763051@rob.eddelbuettel.com>
References: <CAO1zAVam+3Urckfga-OTSp7Fci9nCgfbD5CdNqyyJn_aoSfdVQ@mail.gmail.com>
 <03bff17f-0f25-57e1-61da-1a2235da978b@daqana.com>
 <23561.15485.544650.763051@rob.eddelbuettel.com>
Message-ID: <CAO1zAVbkBuo+0KhyVZkv=45jKFS589OnNj7Sb6OQXeUmLVNSoQ@mail.gmail.com>

I'm sorry, I should have indeed given a better description.

The package I'm seeing the issue with, can be found here :
https://github.com/CenterForStatistics-UGent/RCM

The problem becomes visible when opening an RStudio session and running
BiocCheck::BiocCheck() (This is a Bioconductor package)

> BiocCheck::BiocCheck()
This is BiocCheck version 1.18.0. BiocCheck is a
work in progress. Output and severity of issues may
change. Installing package...
* Checking vignette directory...
    This is a software package
    # of chunks: 39, # of eval=FALSE: 4 (10%)
* Checking version number...
    Checking version number validity...
    Package version 0.99.0; pre-release
* Checking R Version dependency...
* Checking package size...
        Skipped... only checked on source tarball
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      '.git/objects/pack/pack-92e66ff77b78e7fa5121747871adeaa41fb1feb6.pack'
...

And at this point I start hitting myself so I can utter an apology and
inform you that BiocCheck doesn't check filesize on the installed package
but on the original project directory.

My mistake, and I should have been more careful before bothering you all.
Cheers
Joris


On Thu, Dec 6, 2018 at 4:14 PM Dirk Eddelbuettel <edd at debian.org> wrote:

>
> On 6 December 2018 at 15:59, Ralf Stubner wrote:
> | On 06.12.18 15:19, Joris Meys wrote:
> | > I know this R CMD build ignores these files and folders by default,
> but R
> | > CMD INSTALL doesn't apparently.
> |
> | to me this is not apparent. I just tried "R CMD INSTALL ." in a package
> | directory with a .git directory. This went without any problems. What do
> | you observe?
>
> Seconded. I joked off-list to Joris that this post failed to contain a MCVE
> (== minimally complete verifiable example).  Witness below -- two
> installations from a directory containing .git yet none in the installed
> directory.  Could what you describe be particular to your OS or filesystem?
>
> edd at rob:~/git/dang$ ls -a
> .          dang_0.0.7.tar.gz  dang.Rproj   .gitignore  R
> .Rhistory
> ..         dang_0.0.8.tar.gz  DESCRIPTION  man         .Rbuildignore
> .Rproj.user
> ChangeLog  dang.Rcheck        .git         NAMESPACE   README.md
> .travis.yml
> edd at rob:~/git/dang$ R CMD INSTALL .
> * installing to library ?/usr/local/lib/R/site-library?
> * installing *source* package ?dang? ...
> ** R
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (dang)
> edd at rob:~/git/dang$ ls -a /usr/local/lib/R/site-library/dang/
> .  ..  DESCRIPTION  help  html  INDEX  Meta  NAMESPACE  R
> edd at rob:~/git/dang$ install.r
> * installing *source* package found in current working directory ...
> * installing *source* package ?dang? ...
> ** R
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (dang)
> edd at rob:~/git/dang$ ls -a /usr/local/lib/R/site-library/dang/
> .  ..  DESCRIPTION  help  html  INDEX  Meta  NAMESPACE  R
> edd at rob:~/git/dang$
>
>
> Dirk
>
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g>

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http://www.biowiskundedagen.ugent.be/

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[Rd] Dealing with .git folder when using R CMD INSTALL
Joris Meys