I have been able to make it work now, sorry for the previous email.
Best,
Leandro.
On Mon, Feb 12, 2018 at 4:52 AM, Leandro Roser wrote:
>
> Dear BioC,
>
>
> Using the devel version of Biostrings (2.47.9) i am obtaining an error
> message with the 'reverse' function (below an example):
>
>
>
Dear all,
I'm unable to push my recent changes to FamAgg to the Bioconductor git repo
(see below for the error message). I did try the suggested fix but without any
success - seems the duplicated commits are in Bioconductor and not github.
thankful for any help or advise
The error message is:
Dear all,I am trying to build a package for RNA-seq analysis combining
different existing packages in bioconductor and am facing problem while trying
to run Check PackageThere is no error but a warning saying
checking Rd cross-references ... WARNING
Missing link or links in documentation object '
Hi Herve,
The updates have indeed solved those issues for that sample -- However,
when you try to apply a more complicated function, I am getting the same
error. Here's a reproducible example of the error again, this time using
the latest GenomicRanges and IRanges packages:
library(GenomicRa
On 02/12/2018 07:01 AM, Claris Baby via Bioc-devel wrote:
Dear all,I am trying to build a package for RNA-seq analysis combining
different existing packages in bioconductor and am facing problem while trying
to run Check PackageThere is no error but a warning saying
checking Rd cross-referenc
Hi Bioc team,
I'm currently maintaining the packages Ballgown and polyester. However,
I haven't been able to access the new system since the change in system.
I'm wondering if I would be able to be give access? I have included the
maintainers on file for those packages as well.
Best,
Jack
__
Hi Jack,
Have you gone through the steps outlined here?
https://bioconductor.org/developers/how-to/git/
Specifically, have you added ssh keys?
https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
If you have not added keys, you'll need to. Th
Hi,
Try the following. Just print "bed.fn" to see if they are imported
correctly. And use "snpgdsBED2GDS(... verbose=TRUE)" to print more
detailed information or error log.
Qian Liu
Bioconductor Core Team
Roswell Park Cancer Institute
library(SNPRelate)
(bed.fn <- system.file("extdata", "plinkh
Hi Nathan,
You're right, there was a remaining issue. It should be fixed in
IRanges 2.13.26. Make sure to also get S4Vectors 0.17.32 (IRanges
2.13.26 requires it).
The 2 updated packages should become available via biocLite() in
about 24 hours but you can get them now directly from
git.bioconduc
Valerie,
I'm not sure I understand. I looked at another package that is
currently installed on the mac devel machine, DiagrammeR
(https://cran.r-project.org/package=DiagrammeR), and it has the same set
of links on the CRAN site as rsvg does. In particular, it does not show
a r-devel versi
Andrzej,
Sorry, I didn't realize that line was coming from my own Makefile.
The Makefile was there for historic reasons, but I think can be removed
now, so that will probably fix the problem.
Kevin
On 02/08/2018 02:39 AM, Andrzej Oleś wrote:
> Dear Kevin,
>
> thank you for reporting the pr
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