possible package naming conflict
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Entering edit mode
Tobias ▴ 30
@tobias-24288
Last seen 3 months ago
Switzerland

Dear bioconductor,

we would like to submit an R package to bioc available at

https://github.com/fgcz/rawR

A corresponding manuscript is available from

https://www.biorxiv.org/content/10.1101/2020.10.30.362533v1.full

Unfortunately, we recently didn't check for conflicting package names on CRAN and meanwhile a package with a similar name was accepted:

https://cran.r-project.org/src/contrib/Archive/rawr/

p@fgcz-148:~/__checkouts/R > R CMD build rawR && R CMD check rawR_0.1.5.tar.gz --as-cran
* checking for file 'rawR/DESCRIPTION' ... OK
* preparing 'rawR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory 'rawR/src'
* building 'rawR_0.1.5.tar.gz'
* using log directory '/home/cp/__checkouts/R/rawR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'rawR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rawR' version '0.1.5'
* package encoding: UTF-8
* checking CRAN incoming feasibility ...
ERROR
Maintainer: 'Christian Panse <cp@fgcz.ethz.ch>'
New submission
Conflicting package names (submitted: rawR, existing: rawr [https://CRAN.R-project.org])
Conflicting package names (submitted: rawR, existing: rawr [CRAN archive])
...


Since the manuscript & GitHub repo. is already online and made it into blogs and social media, we of cause would like to prevent having to rename our package for bioc submission. Is this possible somehow? We also expected that checks would happen in a case sensitive manner.

"rawR" != "rawr"


according to

“Package:” field: This is the name of the package. This should match the github repository name and is case sensitive. A package name should be descriptive and not already exist as a current package (case-insensitive) in Bioconductor or CRAN. Avoid names that are easily confused with existing package names, or that imply a temporal (e.g., ExistingPackage2) or qualitative (e.g., ExistingPackagePlus) relationship."

proteomics • 795 views
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Entering edit mode

Ahhh...I just realized that the cross check with CRAN is "case-INsensitive". Sorry! OK, but still, is there a way to resolve the conflict without having to clone our package under a different name?

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Entering edit mode

Hi,

Good news to have a way to read RAW file from Thermo directly with R.

Bioconductor covers a large number of research fields nowadays. IMHO, a good name should reflect the field and the goal of the package. As a user, I don't think that a clear and long name will prevent me from using a package. A name with Mass Spectrometry (ms) and Thermo keywords makes more sense to me, as for example the readBrukerFlexData package.

My two-cents

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Entering edit mode

Hi,

thx for your suggestions, but our problem is not really about choosing a good package name (I guess one could discuss this topic for hours and we decided for an onomatopoetic term). Our problem is that our package is already circulating within the proteomics community. If we change the package name just to resolve a conflict with CRAN, we might confuse a lot of people that are already active users.

Best, Tobi

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Entering edit mode

Imho if you want to have the package available at CRAN /Bioconductor the sooner you change the name it the better (less know, less users, less dependencies than if you wait). Just for future cases, there is the package available that checks if a name is available on CRAN, Bioconductor and for possible second meaning names.

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Entering edit mode
@martin-morgan-1513
Last seen 20 days ago
United States

Unfortunately, you are out of luck -- you cannot use rawR as a package name in CRAN / Bioc now that rawr already exists in CRAN. Packages on CRAN / Bioconductor can't have the same name, because for instance BiocManager::repositories() points to available packages from both CRAN & Bioconductor, and there is no way to distinguish packages with the same name. The case insensitivity comes from some file systems (e.g., macOS) that don't distinguish case -- a file or folder 'Foo' and 'foo' are treated as equivalent, and packages are installed as folders on the file system.

A simple way to check for availability is to try to install your future package -- BiocManager::install("rawR"), which will indicate that a similarly named package already exists.

I agree with SamGG that a longer, descriptive name is better all round than a shorter clever name, and with Lluís that it's better to pull this bandage off quickly!

Questions about Bioc package development should really be addressed to the bioc-devel mailing list.

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Entering edit mode

Hi Martin,

Thanks for the clarification. If there is no workaround, we will have to make the cut.

Best, Tobi