CRAN release?

[jefferis]

Is there anything blocking a CRAN release? I notice that there was recently a spam update – not sure if it fixed anything.

[jdmanton]

I think I can implement #7 and add some tests for the spam sparse matrices, ready for a CRAN submission tomorrow. Would it be useful to temporarily change the maintainer field in DESCRIPTION, as we did for nat.templatebrains?

[jefferis]

Take your time!

Fine to change maintainer

[jdmanton]

Initial submission with dad9f5a.

CRAN may complain about

* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'nat:::plot3d.character'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.

but there does not appear to be an easy way of fixing this without modifying exports from nat.

[jdmanton]

As expected, CRAN are not happy:

• checking dependencies in R code ... NOTE

Unexported object imported by a ':::' call: 'nat:::plot3d.character' See the note in ?::: about the use of this operator. See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual.

Please fix.

• checking R code for possible problems ... NOTE

nblast: no visible binding for global variable 'smat_alpha.fcwb' nblast: no visible binding for global variable 'smat.fcwb'

Please fix.

• running examples for arch 'i386' ... [16s] OK

Examples with CPU or elapsed time > 5s user system elapsed create_scoringmatrix 8.54 0.15 8.69

Please reduce to less than 5 sec.

[jefferis]

Plot3d.character should be exported but shouldn't need to be called specifically. Isn't plot3d enough?

smat: are they lazy loaded by Description?

Gregory Jefferis

On 19 Sep 2014, at 00:07, James Manton notifications@github.com wrote:

As expected, CRAN are not happy:

checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'nat:::plot3d.character' See the note in ?::: about the use of this operator. See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual.

Please fix.

checking R code for possible problems ... NOTE nblast: no visible binding for global variable 'smat_alpha.fcwb' nblast: no visible binding for global variable 'smat.fcwb'

Please fix.

running examples for arch 'i386' ... [16s] OK Examples with CPU or elapsed time > 5s user system elapsed create_scoringmatrix 8.54 0.15 8.69

Please reduce to less than 5 sec.

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[jdmanton]

Isn't plot3d enough?

Not quite. I haven't had chance to look into it properly yet, but I guess it's something to do with the substitution-preventing-lazy-evaluation-in-wrong-namespace aspect of how it is called.

smat: are they lazy loaded by Description?

DESCRIPTION has LazyData: yes and the matrices are documented in DATA.r. I'm not given any warning about them when check()ing with devtools, but I'll investigate further later. I guess this is another case of devtools being a bit too clever / insufficiently clever when it comes to namespaces.

[jdmanton]

Resubmitted with 85b6eb3.

[jdmanton]

On CRAN now.

[jefferis]

Great! Thanks a lot, Greg.

Gregory Jefferis

On 19 Sep 2014, at 14:07, James Manton notifications@github.com wrote:

On CRAN now.

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