Re: [Bioc-devel] need advice on how to fix build error in windows

Just wait; this is caused by failures upstream of the pd package; partly at least by affxparser which I maintain (and which was fixed yesterday; hurray). Hopefully this will get sorted out soon; a lot of people are trying to work hard to fix this. Kasper On Fri, Apr 8, 2016 at 5:36 PM, Dan

Re: [Bioc-devel] Feedback on OrganismDb development

On 04/08/2016 02:34 PM, Obenchain, Valerie wrote: > Hi, > > It sounds like we have agreement on these points: > > - Add support for sequences > - Keep the OrganismDb name > - Do provide pre-built packages > > I'm not sure we got much weigh in on the package name. I tend towards a > more

[Bioc-devel] Bioconductor 3.3 release: annotation summary

Hi, This is a heads up about a few changes we've made to the production of in-house annotations for Bioconductor 3.3. # Microarray packages: We will propagate but no longer rebuild the ChipDb, probe and cdf packages. These data have been static for some time. The packages will continue to be

Re: [Bioc-devel] need advice on how to fix build error in windows

It's fine in today's build report. Dan On April 8, 2016 1:31:24 PM PDT, Krithika Bhuvaneshwar wrote: >Dear Biconductor team, > >We are developers of newly accepted Bioconductor package CINdex. Our >package is meant for DNA copy number data analysis, and the example >data

Re: [Bioc-devel] Feedback on OrganismDb development

Hi, It sounds like we have agreement on these points: - Add support for sequences - Keep the OrganismDb name - Do provide pre-built packages I'm not sure we got much weigh in on the package name. I tend towards a more descriptive name. This post (to me) is an example of the confusion that can

[Bioc-devel] need advice on how to fix build error in windows

Dear Biconductor team, We are developers of newly accepted Bioconductor package CINdex. Our package is meant for DNA copy number data analysis, and the example data we use is from Affymetrix SNP 6.0 , so we use 'pd.genomewidesnp.6' annotation package for Affymetrix SNP 6.0 in our vignette. Our

Re: [Bioc-devel] Feedback on OrganismDb development

Dear Valerie, Thank you for the update. 1) Class name: I'd definitely prefer the exisiting naming over the three other suggestions you gave. 2) Pre-made packages: Yes, I think it would be great to have such packages available for well-established Bioc model organisms, i.e. as returned by

Re: [Bioc-devel] rhdf5 and left-justified output in h5ls - is this sensible?

Dear List, Bernd; I've noticed that h5ls now left-justifies its output. For example, if I were to run example(h5ls) on my BioC-devel system, I would get: group name ltype corder_valid corder cset otype num_attrs 0 /fooH5L_TYPE_HARDFALSE 00