This conversation has moved to the community-bioc slack, where the
recommendation is to use BiocFileCache to manage the download. Martin
On 7/29/19, 10:42 AM, "Bioc-devel on behalf of Shraddha Pai"
wrote:
Hi,
Our software package relies on a Java jar file that is 11Mb in size and
This list is intended for questions about package development. The correct
forum for usage questions is at support.bioconductor.org. Please repost
your question over there.
Best,
Jim
On Mon, Jul 29, 2019 at 4:32 PM Jaehyun Lee wrote:
> Hello,
>
> My name is Jaehyun Lee, an undergraduate stud
Hello,
My name is Jaehyun Lee, an undergraduate student at Carnegie Mellon
University conducting developmental biology research. I am currently trying
to run CAGEr using bam files from the CAGE experiment and from my own
reference genome. However, the specific genome that I need is not available
i
Hi Bioconductor team, can you please help with this issue?
Koustav Pal, PhD
Post-Doctoral Fellow in Genome Architecture,
Computational Genomics Group,
IFOM - The FIRC Institute of Molecular Oncology,
Via Adamello 16,
20139 Milano, Italy.
Phone: +393441130157
E-mail: koustav@ifom.eu
> On 2
Surprisingly, if I design the package such that the stan models are
compiled only at run-time I get no issues -> all servers build the
package correctly.
(https://github.com/Bioconductor/Contributions/issues/1187)
On the other hand, if I follow the rstan instructions on how to design
an R pack
My understanding - and I could be wrong - is that Stan compiles a model, so
the compiler needs to be available at run time and not just at build time.
On Thu, Jul 25, 2019 at 4:02 PM Simo Kitanovski
wrote:
> Thanks!
>
> I will try to revise the code to avoid CXX14 if this is that case.
>
> Best
Yes, the badge appears to be correct, but value in the details is incorrect.
Robert
On Mon, Jul 29, 2019, 12:13 PM Shepherd, Lori
wrote:
> Just to verify - The badge at the top is correct but the information in
> the details section at the bottom is showing the incorrect "in
> Bioconductor s
Just to verify - The badge at the top is correct but the information in the
details section at the bottom is showing the incorrect "in Bioconductor since"
time.
I will investigate how this section determines the value and make sure it is
consistent with the badge as this information seems c
Can confirm this is affecting other package pages too. See this on my own
package as well. 3.8 shows 7 years, and then 3.9 and 3.10 show < 6 months.
http://bioconductor.org/packages/3.10/bioc/html/categoryCompare.html
Cheers,
-Robert
Robert M Flight, PhD
Bioinformatics Research Associate
Puller
Hi,
My package HiCBricks is producing build errors on malbec1 and merida1, but
build has passed on tokay1. The corresponding build on travis-ci has also
passed. I can also confirm that the last commits on travis is the same as that
on the bioconductor build machines.
Herein, is the build log
Hi,
The package pages seem to have lost memory
when a package was introduced:
http://bioconductor.org/packages/3.7/bioc/html/xcms.html
http://bioconductor.org/packages/3.8/bioc/html/xcms.html
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 13.5 years)
but now it has reset to:
http://bi
Your package is building clean on the RELEASE_3_9 branch. What are you
updating?
This is clean:
http://bioconductor.org/checkResults/release/bioc-LATEST/MACPET/
The branch that is failing and that needs to be updated is the current
Bioconductor devel (3.10) branch. That branch is the "mast
I have been trying to push the updates on RELEASE_3_9, but they don’t seem to
get updated. They are only updated on GitHub.
Best,
Ioannis
17. jul. 2019 kl. 12:50 skrev Martin Morgan
mailto:mtmorgan.b...@gmail.com>>:
Bioc devel prepares for the next release of bioc, using the version of R that
Hi,
Our software package relies on a Java jar file that is 11Mb in size and
there is a good chance we cannot make the file size smaller. The jar file
is used to run our algorithm so none of the vignettes can run without it
and a separate download would be tedious for users.
Is there still a way to
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