Dear Bioconductor developers,
Some issue with the software builds prevents us from having a build
report today for BioC 3.10. Things should get back to normal tomorrow.
Sorry for the inconvenience.
Cheers,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
This is (was) a bug in data.table that is similar to one which was
putatively closed. Recommend you update to the latest version and if the
problem persists reopen the issue here
https://github.com/Rdatatable/data.table/issues/3032
This mailing list is for R bugs, which this isn’t. R Core can no
On 11/1/19 5:24 PM, Anshul Saravgi wrote:
> Thanks Tomas for identifying the bug.
>
> *How to resolve this bug? Can you please help me here?*
I would recommend you first try to create a complete reproducible
example (the code below is just a snippet). Then try to minimize it -
make it do as
To push to your github branch
git push origin master
To push to the Bioconductor git server and have changes active in Bioconductor
devel
git push upstream master
The upstream master branch is equivalent to whatever the current devel branch
is on Bioconductor (in this case Bioc 3.11).
On 11/1/19 1:11 PM, Anshul Saravgi wrote:
Hi All
Can you help me understand the meaning of the below error message then I
will try to figure out what is going wrong:
*Input Code:*
bodlane2 <- lapply(
+ lapply(split(lctolc2, lctolc2$Item), function(x) graph.data.frame(x[,
2:3])),
+
Hi All
Can you help me understand the meaning of the below error message then I
will try to figure out what is going wrong:
*Input Code:*
> bodlane2 <- lapply(
+ lapply(split(lctolc2, lctolc2$Item), function(x) graph.data.frame(x[,
2:3])),
+ function(x) lapply(
+ V(x)[degree(x, mode =
Thank you all for your valuable comments.
Best,
Jan
On Fri, Nov 1, 2019 at 8:15 PM Tierney, Luke wrote:
>
> On Fri, 1 Nov 2019, Jan Gorecki wrote:
>
> > Thank you Luke.
> > That is why I don't use Rf_inherits but INHERITS which does not
> > allocate, provided in the email body.
>
> Your
If your goal is to perform multithreaded computations, why not perform
all necessary interactions with R upfront and then compute only on
primitives? It would help for us to understand your use case.
On Fri, Nov 1, 2019 at 4:26 AM Jan Gorecki wrote:
>
> Dear R developers,
>
> Motivated by
On Fri, 1 Nov 2019, Jan Gorecki wrote:
> Thank you Luke.
> That is why I don't use Rf_inherits but INHERITS which does not
> allocate, provided in the email body.
Your definition can allocate because STING_ELT can allocate.
getAttrib can GC in general. Currently it would not GC or allocate in
Note that your desire is by definition impossible - as your example also shows
checking for S4 inheritance involves evaluation and thus allocation which
cannot be avoided by the dynamic design of S4 inheritance.
Cheers,
Simon
> On Nov 1, 2019, at 9:23 AM, Jan Gorecki wrote:
>
> Thank you
AFAIR getAttrib() can allocate as well. Also, R API functions that do
not allocate today, may allocate in the future.
Gabor
On Fri, Nov 1, 2019 at 1:24 PM Jan Gorecki wrote:
>
> Thank you Luke.
> That is why I don't use Rf_inherits but INHERITS which does not
> allocate, provided in the email
Hello all,
I am a bit confused by how git works with bioc ecosystem. I am following
this guide to sync my github + bioc repos (for the first time).
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
After step-6, I see following branches
* master
remotes/origin/HEAD
Thank you Luke.
That is why I don't use Rf_inherits but INHERITS which does not
allocate, provided in the email body.
I cannot do similarly for S4 classes, thus asking for some API for that.
On Fri, Nov 1, 2019 at 5:56 PM Tierney, Luke wrote:
>
> On Fri, 1 Nov 2019, Jan Gorecki wrote:
>
> > Dear
On Fri, 1 Nov 2019, Jan Gorecki wrote:
> Dear R developers,
>
> Motivated by discussion about checking inheritance of S3 and S4
> objects (in head matrix/array topic) I would light to shed some light
> on a minor gap about that matter in R C API.
> Currently we are able to check inheritance for
Dear R developers,
Motivated by discussion about checking inheritance of S3 and S4
objects (in head matrix/array topic) I would light to shed some light
on a minor gap about that matter in R C API.
Currently we are able to check inheritance for S3 class objects from C
in a robust way (no
> peter dalgaard
> on Thu, 31 Oct 2019 23:04:29 +0100 writes:
> Hmm, the problem I see here is that these implied classes are all
inherently one-off. We also have
>> inherits(matrix(1,1,1),"numeric")
> [1] FALSE
>> is.numeric(matrix(1,1,1))
> [1] TRUE
>>
On 10/31/19 12:58 AM, Toby Hocking wrote:
Hi all, I am getting an "invalid multibyte string" error from one of my
examples when it is run on solaris, which results in check FAILURE:
https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/nc-00check.html
To fix this I guess I could just
> Pages, Herve
> on Thu, 31 Oct 2019 21:02:07 + writes:
> On 10/30/19 04:29, Martin Maechler wrote:
>>> Gabriel Becker
>>> on Tue, 29 Oct 2019 12:43:15 -0700 writes:
>>
>> > Hi all,
>> > So I've started working on this and I ran into something
Indeed, it's amazing. Thank you, Lori and core team.
Il gio 31 ott 2019, 1:11 PM Sean Davis ha scritto:
> Huge kudos to the team for another successful release.
>
> Sean
>
> On Wed, Oct 30, 2019 at 4:54 PM Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
> > Thanks to all developers
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