e Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel on behalf of
> Vincent Carey
> *Sent:* Thursda
Hello,
Recently two of my packages (SC3 and scmap) started failing checks due to:
"there is no package called ‘BiocStyle'' error. I've added "Suggests:
BiocStyle" into my DESCRIPTION file both on the devel and RELEASE_3_17 as
was advised in the corresponding email and bumped the versions. However,
Hello,
We have a warning related to defining an S4 object:
Warning: undefined slot classes in definition of "MyObject": index(class
"Rcpp_ModuleClass")
More details are here:
https://stackoverflow.com/questions/53814548/rcpp-class-wrapped-in-s4-object-warning
Could anyone please help?
Many than
Thanks Herve!
Cheers,
Vlad
On Wed, Nov 29, 2017 at 6:38 PM Hervé Pagès wrote:
> Hi Vladimir,
>
> On 11/28/2017 01:25 PM, Vladimir Kiselev wrote:
> > Hi Herve,
> >
> > Thanks for your reply! scmap::getSankey() didn't really work in the
> > release, so I swi
ires a higher version of pandoc
> in order to work properly, then maybe you could suggest them to update
> the SystemRequirements field, which is currently:
>
>SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org
>
> (in both, rmarkdown 1.8 and 1.8.3)
>
> Best,
> H.
>
&
Hi,
I am not able to plot Sankey diagrams using `googleVis` in the vignette of
my package (scmap). Here is error message:
http://bioconductor.org/checkResults/devel/bioc-LATEST/scmap/malbec2-buildsrc.html
It says:
pandoc: Could not fetch
https://www.google.com/jsapi?callback=displayChartSankeyID6
Hi,
In my package's (scmap) vignette I plot a Sankey digram using gvisSankey
function from googleVis package. It used to work and the digram was
plotted, but now there is this error (on devel branch -
http://bioconductor.org/checkResults/devel/bioc-LATEST/scmap/malbec1-buildsrc.html
):
pandoc: Co
gt; resubmit on the google-form.
>
> It is run manually at the moment at noon EST everyday.
>
> Nitesh
> > On Sep 11, 2017, at 1:12 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
> >
> > Thanks Simina,
> >
> > I think I've
e submission repo will not get you what you want and is
> only for new packages.
>
> Sean
>
>
> On Mon, Sep 11, 2017 at 1:01 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hi Simina,
>>
>> Thanks for your quick reply, but it looks like to
the helpful advice I
> got from Sean:
>
> Hi, Simina.
>
> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to push a new version of my package to git.bioconductor.org.
>> I
&g
Hello,
I am trying to push a new version of my package to git.bioconductor.org. I
was able to do that in the past. But I've recently changed my public key
and not sure whether this causes a problem. However, I can see my new
public key here - https://github.com/wikiselev.keys - and it is the first
Hi Andrew,
I solved it by just adding '--allow-unrelated-histories' to force the merge:
https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories
Cheers,
Vlad
On Thu, Jul 27, 2017 at 9:53 PM McDavid, Andrew <
andrew_mcda...@urmc.rochester.edu> wrote:
> Is there a re
Hi Martin,
Many thanks for the information.
Cheers,
Vlad
On Wed, Jun 28, 2017 at 3:06 PM Martin Morgan
wrote:
> On 06/28/2017 10:01 AM, Vladimir Kiselev wrote:
> > Hi,
> >
> > Seems I can't find the R-3.5.0 devel build for macOS here:
> > http://r.research.att
Hi,
Seems I can't find the R-3.5.0 devel build for macOS here:
http://r.research.att.com/
Is it ok? Is there any other place I can download it?
Many thanks in advance,
Cheers,
Vlad
--
http://genat.uk
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___
Hi Lorenzo,
Yes, you are right, nothing happens until you bump the version. Now you
need to wait until the next build (usually next day).
Cheers,
Vlad
On Mon, Apr 10, 2017 at 5:17 PM Lorenzo Farina
wrote:
> Hi,
>
> Several days ago I made a minor commit (I updated the author email
> address) t
Hi Wellinton,
As far as I know if you wrap you shiny stuff into an R function that should
be enough. Then you can provide both non-interactive and interactive
functions and the user can choose what to run.
You can have a look at my SC3 package where I implemented a strategy above:
https://github.
this:
#include
using namespace arma;
For the record, here is a link to this issue on GitHub:
https://github.com/hemberg-lab/SC3/issues/33
Many thanks again,
Cheers,
Vladimir
On Thu, Jan 5, 2017 at 7:32 PM Martin Morgan
wrote:
> On 01/05/2017 11:10 AM, Vladimir Kiselev wrote:
> > De
Maybe 1.0.4 is smaller than 1.0.30? Try to change to 1.0.31.
On Fri, 6 Jan 2017, 05:32 Anand MT, wrote:
> Hi Vincent,
>
> Thanks for reply. I swear this was OK till yesterday for updated version!
> This "file not found" issue often occurs but it resolves by itself during
> next builds. Anyways,
nclude
#include
using namespace arma;
using namespace Rcpp;
Many thanks in advance,
Kind regards,
Vladimir
On Thu, Jan 5, 2017 at 12:19 PM Martin Morgan
wrote:
> On 01/05/2017 06:41 AM, Vladimir Kiselev wrote:
> > My package (SC3 -
> http://bioconductor.org/packages/3.4/bioc/html/
Great, many thanks Martin!
On Thu, Jan 5, 2017 at 11:22 AM Martin Morgan
wrote:
> On 01/05/2017 06:16 AM, Vladimir Kiselev wrote:
> > Dear All,
> >
> > After pushing a new version of a package to bioc-devel the vignettes are
> > rebuilt, but I cannot find on which
My package (SC3 - http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
has a function that causes R version/platform-dependent seqfault. Here is
the function (it's in C++ using RccpArmadillo):
arma::mat norm_laplacian(arma::mat A) {
A = exp(-A/A.max());
arma::rowvec D_row = pow(sum(A),
Dear All,
After pushing a new version of a package to bioc-devel the vignettes are
rebuilt, but I cannot find on which platform they were built on. Is it
linux, windows or mac?
Thanks,
Vladimir
--
http://genat.uk
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