Hi, Martin, Val, and Herve.
This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments. Perhaps this is related to some bitnames
being deprecated?
Thanks,
Sean
library(GenomicAlignments)
sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate = FALSE))
x =
This should be fixed now (thanks Martin).
We recently deprecated the flag 'isNotPrimaryRead' in favor of
'isNotPrimaryAlignment' (Rsamtools devel). This affected
GenomicAlignments and others ...
~/b/Rpacks$ grep -lr isNotPrimaryRead *
CoverageView/R/cov.matrix.R
CoverageView/R/cov.interval.R
Hi,
On 12/14/2014 01:29 PM, Valerie Obenchain wrote:
This should be fixed now (thanks Martin).
We recently deprecated the flag 'isNotPrimaryRead' in favor of
'isNotPrimaryAlignment' (Rsamtools devel).
The new name is actually isSecondaryAlignment.
H.
This affected
GenomicAlignments and
R fails to build with visibility on and gcc 4.9's link time optimzation, because
of its practice of building part of it as archive first. Specifically
it builds some bundled libraries as archive first, the symbols of which
are then entirely invisible in gcc 4.9.
The Matrix package also does this
On Thu, Dec 11, 2014 at 12:13 PM, Janko Thyson janko.thy...@gmail.com
wrote:
I'd so much appreciate if someone could have a look at this. If I can be of
any help whatsoever, please let me know!
Your current code uses various functions from XML and rvest so it is not a
*minimal* reproducible
Janko and I have been in touch.
This is, I believe, a Windows specific issue and a compilation issue.
I could be wrong, but that is my impression from other reports.
When I have time (?! :-)), I will deal with it. Hopefully this will
be very soon.
Thanks Janko.
D.
On 12/14/14, 7:54 PM,
On Sun, Dec 14, 2014 at 8:07 PM, Duncan Temple Lang
dtemplel...@ucdavis.edu wrote:
Janko and I have been in touch.
This is, I believe, a Windows specific issue and a compilation issue.
If it does not appear on other systems, it might be the windows build
of libxml2 (or one of the dozens of
