Dear Bioconductor Core Team,
The bumphunter package is exhibiting errors under the Linux and Windows
platforms due to a file download failure from the GENCODE FTP server at the
time of the daily multi-platform build/check testing for BioC 3.14.
*https://bioc.ism.ac.jp/packages/checkResults/devel/b
The release branch has been frozen.
http://bioconductor.org/developers/release-schedule/
Best,
Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute
> On Oct 25, 2021, at 10:28 AM, Federico, Anthony, Nicholas
> wrote:
>
> Hi Nite
There is no need to do it in MulticoreParam as it will simply fork
your master process and therefore inherit your global setting. I think
the warning you get is due to a bug in RStudio, I hope they can fix it
but it might not be that fast...
Best,
Jiefei
On Mon, Oct 25, 2021 at 8:16 PM Giulia Pai
Sorry, my bad, I actually changed the code but for it work properly it is
mandatory to rebuild the package completely (not only loading it through
devtools). It seems to work for 1 function, I'll change the option export
global in all the code and rebuild it and see if it works. Do you know if i
I do not see it from the build report here:
http://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/riesling1-checksrc.html
Can you please provide a reproducible example? It can be very helpful
to locate the issue
On Mon, Oct 25, 2021 at 7:53 PM Giulia Pais wrote:
>
> I mean that tryi
I mean that trying to modify the code of one of the functions that raises
errors and setting the option "exportglobals = TRUE" on SnowParam, somehow it
still fails and says it doesn't find the function "mandatory_is_vars()" which
is a function exported by the package
On 10/25/21, 13:49, "Jiefe
What do you mean by "exported functions are invisible to SnowParam
workers"? Please provide more details. If you call 'bplapply' with a
function from your package, it should be visible to the worker.
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Hello Bioconductor developers,
We are still on track for Bioconductor Release 3.14 for this Wednesday October
27th. This means that tonight is the last day to commit changes to the devel
branch before creating of the RELEASE_3_14 versions of your packages. And any
changes you make to your pac
I tried that also on other functions but it seems also exported functions are
invisible to SnowParam workers. That is really odd since it worked just fine
before. For now since we're approaching the deadline for the new Bioc release
we may opt to switch everything to MulticoreParam despite being
Hi Giulia,
One of your errors is raised from L1288 in the file "analysis-functions.R"
if (getOption("ISAnalytics.verbose") == TRUE) { ... }
The error message is "argument is of length zero". Usually, this means
something is wrong with the global option. Then I see at L4812 in
"internal-functions
Hello,
I�m the developer of the package ISAnalytics. Since the last build we�re having
issues with BiocParallel on the Windows platform only. In particular, trying to
debug what the issue might be on a local Windows machine, it seems BiocParallel
isn�t able to find internal package functions and
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