object 'IMGT_V_NO_CDR3' not found

[David Koppstein]

Hello,

I was installing shm via the command line as per instructions, but came across this issue. Here's the log:

> library(roxygen2)
l> library(devtools)
> roxygenize()
Loading required package: alakazam
Loading required package: ggplot2
Loading required package: plyr
Loading required package: doSNOW
Loading required package: foreach
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Loading required package: iterators
Loading required package: snow
Loading required package: data.table
data.table 1.9.4  For help type: ?data.table
*** NB: by=.EACHI is now explicit. See README to restore previous behaviour.
Loading required package: SDMTools
Loading required package: scales
Loading required package: seqinr
Loading required package: ade4

Attaching package: ‘seqinr’

The following object is masked from ‘package:plyr’:

    count

Loading required package: zoo
ins
Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

tall_deError: Failure in roxygen block beginning RegionDefinitions.R:92
object 'IMGT_V_NO_CDR3' not found
In addition: Warning message:
undefined slot classes in definition of "BASELINe": regionDefinition(class "RegionDefinition")

[Jason Vander Heiden]

We cleaned up a bunch of the roxygen errors and some collate errors. This particular error is hauntingly persistent, and appears to be some sort of weird roxygen bug (or something we can't quite figure it out).

The solution is to build with devtools::document() instead of roxygen2::roxygenise(). Seeing as document() is a wrapper for roxygenise() I'm not sure why this matters... Seems like it might have something to do with LazyData load order. So, can you try:

library(roxygen2)
library(devtools)
document()
install_deps()
build(vignettes=FALSE)
install()

And see if that works for you?

[David Koppstein]

It works, thank you!