An update: the fixed gap package is now in CRAN
(https://cran.r-project.org/web/packages/gap/index.html). Once the Windows
build machine uses/installs this updated CRAN package, the error in FamAgg will
be fixed.
cheers, jo
On 19 Apr 2017, at 13:04, Rainer Johannes
On 04/19/2017 03:33 PM, Astrid Deschenes wrote:
Hi,
The Bioconductor Git mirror
https://github.com/Bioconductor-mirror/methylInheritance returns a 404 error.
Is this normal?
This has been corrected.
The mirror is useful as a way to cite or navigate code, but it's
irrelevant to the
On 04/19/2017 02:45 AM, Michael Stadler wrote:
Dear BioC core,
Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?
Nothing you can do in QuasR itself. Sorry that I don't have time to do
this but someone
Hi Michael,
On 04/17/2017 12:31 PM, Michael Love wrote:
alpine, which had this error as of Sunday, is now cleared (I didn't
make any changes to the code)
Hi Christian,
So I installed ROOT 5 from source on veracruz2. It's in
/usr/local/root.
However, Apple's SIP (System Integrity Protection, new and
enabled by default on El Capitan) is getting in the way when
trying to install xps. That's because xps configure and build
process relies on
Thanks Steffen for bringing this to the R-devel list. I only
see the fix in trunk for now. They'll need to port it to the 3.4
branch if we want to see it propagate to our BioC 3.5 builds.
Just to clarify, by default R doesn't use the -Wall flag to
compile packages on Linux. It's something we add
Hi,
Due to errors / unresponsive maintainers this new group of packages has
been identified for potential deprecation in Biocondcutor 3.5.
anamiR
FunChiP
MutationalPatterns
seqplots
snm
ssviz
stepwiseCM
ToPASeq
If anyone is interested in taking over as maintainer please let us know.
If not
Hi,
just a quick report, I followed this up to r-devel,
and a fix adding -O2 back to default CXXFLAGS
has been committed (r72549, see [1]) to R by Martyn Plummer,
thus "fixing" the abort() related WARNING in mzR/xcms
once this gets into the R version used on malbec2.
Yours,
Steffen
[1]
hi,
got it, the current version on svn of VariantAnnotation (1.21.19) is
ahead of what's available via biocLite(). i've checked out
VariantAnnotation 1.21.19, installed it and the bug has dissapeared.
problem solved.
thanks!
robert.
On 04/19/2017 05:39 PM, Michael Lawrence wrote:
Not
Not reproducing for me. This is with S4Vectors, VariantAnnotation,
etc, from svn.
R Under development (unstable) (2016-12-13 r71785)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8
Dear Martin,
Thank you for the quick response - you are right to suspect bowtie, it
seems that version 1.1.1 which I am using in Rbowtie has an issue on
newer macOS versions, and I am currently looking into wether an update
to version 1.2 would fix this.
A first issue that I stumbled into is
hi,
it seems that recent changes to S4Vectors are breaking the coercion from
the '*VCF' class to the 'VRanges' class. the traceback points to the
private function 'recycleVector() from the 'S4Vectors' package, please
find below the minimal example that reproduces the problem with the
session
Thanks Lori for the info!
Actually, the maintainer of the gap package fixed the problem now in his
package. Once the new version of gap is in CRAN (hopefully soon) the error in
FamAgg will be gone too.
cheers, jo
On 19 Apr 2017, at 12:56, Shepherd, Lori
You can continue to commit changes and bug corrections until this Friday 21.
After that date any change will remain in devel and if necessary would have to
be corrected in release after the release is finished.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department
Dear BioC core,
Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?
I have another question regarding QuasR not building on veracruz2: The
vignette does not build currently, reporting:
Error on
Dear all,
Somehow the FamAgg fails building with the recent R-3.4rc in Windows. I tracked
down the error and it comes from a fortran code in a function from the "gap"
CRAN package I'm using in one of the functions. I contacted the developer and
in the meantime implemented a workaround in
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