Yes, when a new version appears on CRAN it is automatically picked up by the
build machines.
Valerie
On 05/14/2018 05:04 AM, Kevin Horan wrote:
Valerie,
Sorry, I think my memory of what the actual problem was was wrong. I have
spoken to the rsvg author and he has now fixed the build of
Hi Hervé,
Thanks a lot for addressing it!
Best regards,
Jialin
On Tue, 2018-05-15 at 09:02 -0700, Hervé Pagès wrote:
> Hi Jialin,
>
> Thanks for the report. This should be fixed in BioC 3.7 (S4Vectors
> 0.18.2 and IRanges 2.14.10) and BioC devel (S4Vectors 0.19.3 and
> IRanges 2.15.11).
>
> T
One of the CEL files is truncated or otherwise corrupted. The
appropriate place to really detect that is in the code that reads the
CEL file data and appropriately warn or error to the user.
The bug below occurs because of a massive mismatch between the
assumptions of the RMA background model
Dear Nitesh,
Thank you for pointing me to the website how to resolve the conflict.
I hope that now everything is ok.
For the records, here is what I did:
$ cd /Volumes/T3Data/CRAN/GIT/xps
$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
Untracked files:
(use "git
Hi Jialin,
Thanks for the report. This should be fixed in BioC 3.7 (S4Vectors
0.18.2 and IRanges 2.14.10) and BioC devel (S4Vectors 0.19.3 and
IRanges 2.15.11).
The updated packages will become available via biocLite() in the
next 24h (if everything goes as expected).
Best,
H.
On 05/14/2018 07
Hi
You have to fix the merge conflicts. Again, please take a look at the
documentation on the website
The canonical documentation for git:
http://bioconductor.org/developers/how-to/git/
The documentation relevant to your problem:
http://bioconductor.org/developers/how-to/git/resolve-conflict
But ... yes. The package is scheduled to be removed unless it is fixed before
the next release so it is not advisable in its current state to utilize its
functionality.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Car
You could always reach out to the maintainer to try and get them interested
again.
Or reach out on the mailing list or support site to see if anyone else is
interested in taking over maintaining the package.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of
Dear Marcel,
Thank you for the clarification, now it seems to work.
However, there is a strange problem. Here is what I did:
$ cd /Volumes/T3Data/CRAN/GIT/xps
$ git remote -v
origin g...@github.com:cstrato/xps.git (fetch)
origin g...@github.com:cstrato/xps.git (push)
upstreamg...@gi
Hi Christian,
Marcel is correct. The documentation is given here,
http://bioconductor.org/developers/how-to/git/pull-upstream-changes/.
Best,
Nitesh
> On May 14, 2018, at 6:22 PM, Marcel Ramos
> wrote:
>
> Hi Christian,
>
> It looks like you have to do
>
> *git pull upstream master *
>
I guess I should make my package independent of it then, but that's going
to ask some work. That's very unfortunate...
2018-05-15 7:24 GMT-04:00 Shepherd, Lori :
> What is your sessionInfo()? This was corrected in version 1.27.1 of the
> package so you could try updating to that version.
>
>
>
>
What is your sessionInfo()? This was corrected in version 1.27.1 of the package
so you could try updating to that version.
However, htSeqTools is currently deprecated in Release Bioc 3.7 and currently
scheduled to be removed in Bioc 3.8 as the maintainer has be inactive in
maintaining the pa
Kenneth,
You should _always_ run R CMD check (and R CMD BiocCheck) on the tarball
generated by R CMD build. The build step essentially cleans the code. If
your vignette takes a bit to generate (the vignette gets generated with R
CMD build), just do R CMD build --no-build-vignettes
Best,
Kasper
Hi Lori,
Thanks for the reply. The actual tar.gz built by R CMD build is only 3Mb so
maybe I should ignore the note and submit? The note may actually be
referring to large .git objects in the git history - not sure.
Regards,
Kenneth
On Mon, May 14, 2018 at 12:15 PM, Shepherd, Lori <
lori.sheph.
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