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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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2b597eb fails tests #29

Closed amcdavid closed 11 years ago

amcdavid commented 11 years ago

The new data.table constructor has a bunch of issues in the tests (the constructed object is essentially gibberish right now) so I moved that code to devel and reverted master.

Agreed that we need to make RNAseq construction faster. Would writing a constructor that takes an expression matrix and fData and cData be a good solution?

gfinak commented 11 years ago

That would be an excellent solution

On Fri, Oct 25, 2013 at 12:45 PM, Andrew McDavid notifications@github.comwrote:

The new data.table constructor has a bunch of issues in the tests (the constructed object is essentially gibberish right now) so I moved that code to devel and reverted master.

Agreed that we need to make RNAseq construction faster. Would writing a constructor that takes an expression matrix and fData and cData be a good solution?

— Reply to this email directly or view it on GitHubhttps://github.com/RGLab/SingleCellAssay/issues/29 .

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

gfinak commented 11 years ago

Found the bug

On Fri, Oct 25, 2013 at 1:06 PM, Greg Finak gfinak@fhcrc.org wrote:

That would be an excellent solution

On Fri, Oct 25, 2013 at 12:45 PM, Andrew McDavid <notifications@github.com

wrote:

The new data.table constructor has a bunch of issues in the tests (the constructed object is essentially gibberish right now) so I moved that code to devel and reverted master.

Agreed that we need to make RNAseq construction faster. Would writing a constructor that takes an expression matrix and fData and cData be a good solution?

— Reply to this email directly or view it on GitHubhttps://github.com/RGLab/SingleCellAssay/issues/29 .

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

gfinak commented 11 years ago

I believe the latest lme4 package is not compatible with zlm. They've changed object types in the package so tests are failing.

On Fri, Oct 25, 2013 at 1:13 PM, Greg Finak gfinak@fhcrc.org wrote:

Found the bug

On Fri, Oct 25, 2013 at 1:06 PM, Greg Finak gfinak@fhcrc.org wrote:

That would be an excellent solution

On Fri, Oct 25, 2013 at 12:45 PM, Andrew McDavid < notifications@github.com> wrote:

The new data.table constructor has a bunch of issues in the tests (the constructed object is essentially gibberish right now) so I moved that code to devel and reverted master.

Agreed that we need to make RNAseq construction faster. Would writing a constructor that takes an expression matrix and fData and cData be a good solution?

— Reply to this email directly or view it on GitHubhttps://github.com/RGLab/SingleCellAssay/issues/29 .

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

amcdavid commented 11 years ago

Yup, car::lht is broken with lme4 > .9999, and we use lht, so now we're broken.

But those weren't the errors that I was getting (because I still had an old version of lme4).

gfinak commented 11 years ago

Okay, I've fixed the bugs related to data.table. There was a line I missed assigning it to the .Data object. lme4 has a new release which depends on Matrix and has changed the type of object from mer to lmerMod and glmerMod I've adapted the tests to reflect this and added a line to test.zlm to check it. All test passed. Committed to github

On Fri, Oct 25, 2013 at 1:40 PM, Greg Finak gfinak@fhcrc.org wrote:

I believe the latest lme4 package is not compatible with zlm. They've changed object types in the package so tests are failing.

On Fri, Oct 25, 2013 at 1:13 PM, Greg Finak gfinak@fhcrc.org wrote:

Found the bug

On Fri, Oct 25, 2013 at 1:06 PM, Greg Finak gfinak@fhcrc.org wrote:

That would be an excellent solution

On Fri, Oct 25, 2013 at 12:45 PM, Andrew McDavid < notifications@github.com> wrote:

The new data.table constructor has a bunch of issues in the tests (the constructed object is essentially gibberish right now) so I moved that code to devel and reverted master.

Agreed that we need to make RNAseq construction faster. Would writing a constructor that takes an expression matrix and fData and cData be a good solution?

— Reply to this email directly or view it on GitHubhttps://github.com/RGLab/SingleCellAssay/issues/29 .

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA 98109

(206)667-3116 gfinak@fhcrc.org

amcdavid commented 11 years ago

In d4a4afe I isolated the bug in that we introduced and it has test coverage now, but I haven't fixed it yet.