On 02/21/2017 03:24 PM, Levi Waldron wrote:
On Tue, Feb 21, 2017 at 2:02 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi Levi,
Were you able to sort this out? I think we should emphasize the
importance of re-installing packages *from source* (i.e. with
biocLite(..., type="source")). This is because some of the package
binaries we distribute seem to be affected by this problem too.
We're planning to fix these binaries over the next couple of days.
Thank you, Hervé. I hadn't re-installed from source, and haven't gotten
around to doing a complete re-install, so I tried again with
`biocLite(..., type="source")`. But it still didn't fix the problem
re-installing `mydep$phyloseq` above with type="source". It isn't a
great rush, so perhaps I'll just wait until you've updated the binaries.
Here's an attempt to fail when the vectorORfactor class is contained in
'list', which I think is where the problem comes from
trace(
loadNamespace,
quote(print(package)),
exit=quote({
contains <- names(getClass("list")@contains)
if (any(grepl("vectorORfactor", contains)))
stop("found after: ", package)
})
)
library(phyloseq)
Sorry for the inconvenience,
No worries!
-Levi
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