alue_meme.c#L14
It may also cause incompatibility problems with the GPL license of the
whole R package when distributed as a binary package or a container
image.
Best,
Charles, Debian developer and OIST.jp researcher
--
Charles Plessy
http://charles.plessy.org
Nagah
dering if this bug would be a low-hanging
fruit for somebody else in this list?
Have a nice day,
Charles Plessy
--
Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp
Okinawa Institute of Science and Technology Graduate University
Senior staff scientist ~~ Lusc
Hello
on my R 4.1.0 system, rtracklayer version 1.53.1 refuses to load
XZ-compressed GFF files, throwing the error "has unsupported type:
xzfile". As the function's manual page states that xz-compressed files
are handled transparently, I suppose it is a bug?
Have a ncie day,
se.
Before I start to invest time in either direction, I wanted to check on
that mailing list if there were other solutions already existing, in
particularly closer to the core packages ?
Have a nice day,
Charles
--
Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp
Ok
On 15/07/2020 10:53, Charles Plessy wrote:
On 14/07/2020 19:56, Vincent Carey wrote:
Can you post an example dataset that triggers the error reproducibly?
here it is:
https://www.dropbox.com/s/ai9itm586clt4y9/gp.Rds?dl=0
It is a GPos object; interestingly I just realised that export.bw will
to GRanges first...
Thanks for your help, and have a nice day,
Charles
--
Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp
Okinawa Institute of Science and Technology Graduate University
Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu
Toots from
2.1.0operator.tools_1.6.3 beanplot_1.2
[58] memoise_1.1.0VGAM_1.1-3
--
Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp
Okinawa Institute of Science and Technology Graduate University
Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu
= FALSE) one, plus an inializing function so that new()
can promote an UnstitchedGPos to the class, and finally a coerce method
so that GRanges can be converted. The result is here:
https://github.com/charles-plessy/CAGEr/blob/fix-CTSS-GPos/R/CTSS.R
Not sure if you have time to have a look, but an
object in the wrapping class.
Have a nice day,
Charles Plessy
--
Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp
Okinawa Institute of Science and Technology Graduate University
Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu
Toots from
` and `object <- c(object, myExp=value)`
but both of them fail.
2) If I want to update an experiment (for instance because I added a
new assay in a SummarizedExperiment, on which I applied a normalisation
method), what is the most appropriate way ?
Have a nice day,
Charles
--
Charles Ple
a GRanges object
where the ranges are still in UnstitchedIPos class, while in the case of
gpos1a and gpos1b they has been converted.
I do not know how to deal with that problem and I would appreciate some
help.
Have a nice day,
Charles
--
Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - c
<- MultiAssayExperiment(ExperimentList(exp1=rSE)))
(m[[1]] <- m[[1]])
m # No change
(m<- c(m, exp2=SE))
(m[[1]] <- m[[1]])
m # RangedSummarizedExperiment replaced with SummarizedExperiment
sessionInfo()
```
Am I misusing the MultiAssayExperiment objects, or is this a
Thanks you everybody for the help and the reaction,
after MultiAssayExperiment was updated, CAGEr now builds fine.
Have a nice day,
--
Charles
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ll as existing code.
I am lost on how to troubleshoot this. May I ask for your help ?
Best regards,
--
Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp
Okinawa Institute of Science and Technology Graduate University
Staff scientist in the Luscombe Unit - ~ - https:/
lot2_2.2.1 codetools_0.2-15
microbenchmark_1.4-2.1
[25] bitops_1.0-6RCurl_1.95-4.10 sandwich_2.4-0
compiler_3.4.3
[29] scales_0.5.0mvtnorm_1.0-6 zoo_1.8-0
(I have also made a benchmark on "real" data, which
nt, and that piped commands can be harder to debug; therefore
it may be better to only use them in interactive sessions.)
Have a nice day,
--
Charles Plessy
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installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
Obviously, client-side LC_ALL=C suppresses this, but perhaps it can be silenced
server-side, either by supporting many locales, or enforcing the default C
locale without warning.
Have
refBases <- getSeq(geome::genome, Granges)
Hello Zach,
recently, I did something like this:
requireNamespace(genome)
genome <- getExportedValue(genome, genome)
I am not sure if it is the best solution, but for the moment, it works.
Have a nice week-end,
Charles
--
Charles Plessy, Ph.D.
, had no
other change than a regular push.
Have a nice day,
--
Charles Plessy
Tsurumi, Kanagawa, Japan
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