ShortRead imports more than necessary

[benjjneb]

The ShortRead package is importing more than necessary, which adds some time and excess messages during package loading.

Is it possible to import just part of a package? Joey?

[spholmes]

You could require that it is installed and then not require(ShortRead) but
just use
ShortRead::function.

On Thu, Aug 6, 2015 at 10:22 AM, benjjneb notifications@github.com wrote:

The ShortRead package is importing more than necessary, which adds some
time and excess messages during package loading.

Is it possible to import just part of a package? Joey?

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#28.

Susan Holmes
Professor, Statistics and BioX
John Henry Fellow in Undergraduate Education
Sequoia Hall,
390 Serra Mall
Stanford, CA 94305
http://www-stat.stanford.edu/~susan/

[benjjneb]

derepFastq is core functionality though, so shouldn't depend on a require.

On Thu, Aug 6, 2015 at 10:26 AM, spholmes notifications@github.com wrote:

You could require that it is installed and then not require(ShortRead) but
just use
ShortRead::function.

On Thu, Aug 6, 2015 at 10:22 AM, benjjneb notifications@github.com
wrote:

The ShortRead package is importing more than necessary, which adds some
time and excess messages during package loading.

Is it possible to import just part of a package? Joey?

—
Reply to this email directly or view it on GitHub
#28.

Susan Holmes
Professor, Statistics and BioX
John Henry Fellow in Undergraduate Education
Sequoia Hall,
390 Serra Mall
Stanford, CA 94305
http://www-stat.stanford.edu/~susan/

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#28 (comment).

[joey711]

Yes, you should not do a require. While we were prototyping it didn't make sense to worry too much about pairing down the namespace. Now that we're prepping for BioC submission, we absolutely should think about it.

The best-practice approach is to use the importFrom tag in roxygen:

#' @importFrom ShortRead ShortReadMeth

Instead of loading all of ShortRead, we just specify the exact methods within ShortRead that dada2 will use. It's much cleaner, and avoids some collisions among the packages that dada2 depends on.

[benjjneb]

Where does this roxygen incantation go?

Right now the ShortRead import is happening from the "ShortRead (>=
1.24.0)" being included in the Imports: part of the Description file.

On Thu, Aug 6, 2015 at 12:31 PM, Paul J. McMurdie notifications@github.com
wrote:

Yes, you should not do a require. While we were prototyping it didn't
make sense to worry too much about pairing down the namespace. Now that
we're prepping for BioC submission, we absolutely should think about it.

The best-practice approach is to use the importFrom tag in roxygen:

#' @importFrom ShortRead ShortReadMeth

Instead of loading all of ShortRead, we just specify the exact methods
within ShortRead that dada2 will use. It's much cleaner, and avoids some
collisions among the packages that dada2 depends on.

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#28 (comment).