Thanks for these explanations, Martin.
What I actually want to do is sending each expression dataset on probe level to
a worker, where probe level expression is summarized to gene level expression
according to a chosen summarization function (such as 'mean').
The worker should then return the e
On 01/19/2018 02:24 PM, Ludwig Geistlinger wrote:
I apologize if I haven't been specific enough - however, I am also having
trouble to reliably reproduce the error.
It does not seem to be exclusively related to the combination of AnnotationDbi
and parallel computation, but also with some other
I apologize if I haven't been specific enough - however, I am also having
trouble to reliably reproduce the error.
It does not seem to be exclusively related to the combination of AnnotationDbi
and parallel computation, but also with some other packages I load.
While still trying to produce a mi
On 01/19/2018 12:37 PM, Gabe Becker wrote:
IT seems like you could also force a copy of the reference object via
$copy() and then force a refresh of the conn slot by assigning a
new db connection into it.
I'm having trouble confirming that this would work, however, because I
actually can't repro
You want to follow
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
And look at #8 in that page,
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
You should follow this and try once more.
Nitesh
> On Jan 19, 2018, at 12:5
On 01/19/2018 12:23 PM, Vincent Carey wrote:
good question
some of the discussion on
http://sqlite.1065341.n5.nabble.com/Parallel-access-to-read-only-in-memory-database-td91814.html
seems relevant.
converting the relatively small annotation package content to pure R
read-only tables on the ma
The Bioconductor Team is continuing to identify packages that will be
deprecated in the next release to allow for the Bioconductor community to
respond accordingly. The list will be updated monthly.
The current list of deprecated packages is as follows:
Maintainer requested deprecation:
Softw
The pre-receive hook is catching the duplicate commits on your local repository
and preventing the push from contaminating the bioconductor version of the
repository.
If you need help fixing your local repository, feel free to ask questions. Try
to follow the link in error message and see if yo
IT seems like you could also force a copy of the reference object via
$copy() and then force a refresh of the conn slot by assigning a
new db connection into it.
I'm having trouble confirming that this would work, however, because I
actually can't reproduce the error. The naive way works for me on
Hi Laurent,
If you check the package “hpar” with a fresh clone from git@git.bioconductor,
you’ll see that it doesn’t have any duplicate commits now.
I think only your local repository has duplicate commits. You’d have to fix
this issue on your side.
Best regards,
Nitesh
> On Jan 19, 2018,
good question
some of the discussion on
http://sqlite.1065341.n5.nabble.com/Parallel-access-to-read-only-in-memory-database-td91814.html
seems relevant.
converting the relatively small annotation package content to pure R
read-only tables on the master before parallelizing
might be very simple?
Great news!
Thanks Valerie
Best Regards
Yuriy
On Fri, Jan 19, 2018 at 11:40 AM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:
> Hi Krithika,
>
> I believe this was related to a problem with getTable() in rtracklayer:
>
> https://github.com/lawremi/rtracklayer/issues/5
>
> rt
Hi Krithika,
I believe this was related to a problem with getTable() in rtracklayer:
https://github.com/lawremi/rtracklayer/issues/5
rtracklayer 1.39.5 built successfully today and the error in CINdex has cleared
up:
https://bioconductor.org/packages/3.7/bioc/html/CINdex.html
Valerie
O
Hi,
Within a package I am developing, I would like to enable parallel probe to gene
mapping for a compendium of microarray datasets.
This accordingly makes use of annotation packages such as hgu133a.db, which in
turn connect to the SQLite database via AnnotationDbi.
When running in multi-core
Hi all,
I have pushed changes to the DrugVsDisease repository and have been able to
verify these changes are present in the git repository (after adding it to my
GitHub account and checking for the changes). However, it seems that an old
version is still be checked in the daily reports - and ar
Hi Stephan,
The key seems to be correct. You should have read and write access to that
package.
I missed the fact that it was an experiment data package and not a software
package.
Thanks,
Nitesh
> On Jan 19, 2018, at 3:29 AM, Neumann, Steffen wrote:
>
> Hi BioC team,
>
> I have R W for
Bioc developers!
A number of packages in the 'master' branch of their git repository
build and check successfully, but do not propagate to the 'devel'
repository (red light at the extreme right, e.g., ABSSeq; mouse over for
details)
https://bioconductor.org/checkResults/3.7/bioc-LATEST/ABS
Hi BioC team,
I have R W for several packages I am involved in,
but not for mtbls2 that I maintain. Please add W
for "s.neumann" for mtbls2 as well, or is there
any mistake on my side ?
Thanks in advance,
yours,
Steffen
R Wpackages/msdata
R packages/mtbls2
R Wpackages/mzR
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