Welcome
Best,
Kasper
On Sun, May 8, 2016 at 9:48 AM, Martin Morgan wrote:
> Bioc developers,
>
> We're very pleased to welcome Lori Shepherd to the Bioconductor team in
> Buffalo. Lori has a Masters in Bioinformatics and Biostatistics. Her
> background includes sequence analysis, server adminis
Thanks Sean!
It looks like it does build and check. But the last commit was made after the
daily deadline (4:20PM Seattle time) so this won't be available via biocLite()
till Tuesday sometime. It can be installed via git or svn in the meantime.
Dan
- Original Message -
> From: "Sean D
Hi, all.
Sorry for the hiccup. The problem appears to have stemmed from NCBI GEO
switching to using https for GEO data tables. This is not a highly-used
feature, but it was enough to break the build. It should be fixed (cross
fingers) in Devel. If fixed in devel, I will backport to release.
Hi all,
You may have noticed that there are no Mac builds in the new devel
(Bioconductor 3.4) build report.
One of the build macs died.
We have ordered replacement hardware and we hope it will arrive soon. Then
after it is configured, we aim to get Mac builds going again as soon as
possible
Hi Wolfgang,
Yep. All good suggestions. Thanks!
H.
On 05/08/2016 12:52 AM, Wolfgang Huber wrote:
Hervé
Thank you, looks great. Regarding files like
https://bioconductor.org/packages/new-stats/bioc/Biobase/Biobase_2016_stats:
woudln’t it be good to
- provide column headers
- give the file a
GEOmetadb had an issue with Dropbox jerking around URLs (cf
https://github.com/ttriche/simpleSampleSearch/blob/master/R/checkForUpdates.R
); I wonder if this might be related? I'd hate for GEO to become as flaky as
biomaRt.
I should have submitted simpleSampleSearch for 3.3 but it seemed too t
GEOquery is available in release (3.3), though not the most recent version.
Hopefully release and not devel is being used in the edX class; the devel
builds are not yet stable, but should be later today. In any case, it's
early-cycle devel.
Dan
- Original Message -
> From: "Dan Tenenb
Maybe. If the package does not build for many days on end, it's more than
flakiness and one wonders if the service is usable at all.
Tests that indicate this seem appropriate to me, though I agree false positives
can be annoying.
Dan
- Original Message -
> From: "Vincent Carey"
> To: "
Hmm. Very important piece of software so we should try to remedy this. I
had assigned some GEOquery problems in the edX class and there were some
people who could not get getGEO to work, but the problem seemed
intermittent. There was a workaround posted on the support site which
involved separat
It has not built since the devel (3.4) builds started. Apparently GEO has been
pretty flaky.
Dan
- Original Message -
> From: "Kasper Daniel Hansen"
> To: "bioc-devel"
> Sent: Sunday, May 8, 2016 5:54:59 AM
> Subject: [Bioc-devel] GEOquery for Bioc devel
> I don't see GEOquery for Bi
New package developers --
We hope to start the new package submission process
https://support.bioconductor.org/p/76472
as early as May 23, 2016. If you're planning to submit packages to
Bioconductor after that date, please develop your package using a github
repository; we'll use these as t
Bioc developers,
We're very pleased to welcome Lori Shepherd to the Bioconductor team in
Buffalo. Lori has a Masters in Bioinformatics and Biostatistics. Her
background includes sequence analysis, server administration, and R
package development. You might already have seen Lori getting up to
I don't see GEOquery for Bioc devel. Is that a mistake somehow?
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Hervé
Thank you, looks great. Regarding files like
https://bioconductor.org/packages/new-stats/bioc/Biobase/Biobase_2016_stats:
woudln’t it be good to
- provide column headers
- give the file a reasonable extension reminding of its format
- format it such that it can be read with default parame
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