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NESCent / popgenInfo

Vignettes for Population Genetics in R
http://popgen.nescent.org
MIT License
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Fix baseline build errors #87

Closed hlapp closed 8 years ago

hlapp commented 8 years ago

This merges #79 and #85 which together (but not individually) should fix the baseline build errors we've been struggling with due to CRAN package changes.

hlapp commented 8 years ago

OK we've got the next error that hasn't been seen before:

Quitting from lines 67-75 (StartSNP.Rmd) 
Error in eval(expr, envir, enclos) : 
  no slot of name "loc.nall" for this object of class "genind"

How do we fix this? @smanel (attributed author of StartSNP.Rmd) or @zkamvar, any suggestions?

zkamvar commented 8 years ago

Line 72 is the culprit here.

- Mydata1@loc.nall
+ nAll(Mydata1)
zkamvar commented 8 years ago

I'll fix it here and see if that works

hlapp commented 8 years ago

That did work, and now we have the next error:

Quitting from lines 67-75 (StartSNP.Rmd) 
Error in genind2hierfstat(Mydata1) : 
  alleles must be encoded as integers or nucleotides. Exiting

How did we fix this before?

zkamvar commented 8 years ago

I just noticed that there are some issues with data sanitization (adegenet can't handle "." in locus names). I'm going to work on this a little and see if I can produce a fix.

zkamvar commented 8 years ago

I found the problem. It exists within hierfstat.

hlapp commented 8 years ago

I found the problem. It exists within hierfstat.

So hierfstat needs to be fixed and then we switch the container build to installing hierfstat from Github again?

zkamvar commented 8 years ago

So hierfstat needs to be fixed and then we switch the container build to installing hierfstat from Github again?

I think that's about the size of it :frowning:

zkamvar commented 8 years ago

Although, it might pass if we included 12 loci in the data.

hlapp commented 8 years ago

Although, it might pass if we included 12 loci in the data.

Nope, it didn't.

zkamvar commented 8 years ago

actually, it did, but now another error is reeling its ugly head:

Quitting from lines 75-78 (SummarySequenceData.Rmd) 
Error in validObject(x) : invalid class "genind" object: FALSE
Calls: <Anonymous> ... summary -> summary -> .local -> is.genind -> validObject

This one is caused by the fact that Margarita updated her data for PopDiffSequenceData. @mmlopezu, Did you double the number of samples in your data?

zkamvar commented 8 years ago

After looking into it, there are many things that are going to fail in that vignette because it was one of the first ones written back when adegenet still had HWE.test.genind.

I think the main things that need to be removed are the Fst and HW tests, since they require diploids.

Additionally, when adegenet 2.0.1 comes down the line, the names for the summary object will be different -_-

hlapp commented 8 years ago

So perhaps the solution is to remove that vignette here, and to reintroduce it on a development branch, where it can wait until it is fixed. I can do that if that would work for everyone.

smanel commented 8 years ago

Good idea!

zkamvar commented 8 years ago

So perhaps the solution is to remove that vignette here, and to reintroduce it on a development branch, where it can wait until it is fixed. I can do that if that would work for everyone.

I think that works. @mmlopezu, does that work for you?

hlapp commented 8 years ago

That does the trick indeed. I'll merge to master and resolve the conflict.

mmlopezu commented 8 years ago

@zkamvar https://github.com/zkamvar yes, it does work. I'll work on it this weekend.

On Wed, Dec 16, 2015 at 4:35 PM, Zhian N. Kamvar notifications@github.com wrote:

So perhaps the solution is to remove that vignette here, and to reintroduce it on a development branch, where it can wait until it is fixed. I can do that if that would work for everyone.

I think that works. @mmlopezu https://github.com/mmlopezu, does that work for you?

— Reply to this email directly or view it on GitHub https://github.com/NESCent/popgenInfo/pull/87#issuecomment-165247161.

Margarita M. López-Uribe NSF Postdoctoral Fellow Department of Entomology and Department of Applied Ecology North Carolina State University https://sites.google.com/a/cornell.edu/mm-lopez-uribe/ https://sites.google.com/a/cornell.edu/margarita-m-lopez-uribe/

hlapp commented 8 years ago

@mmlopezu - note that this pull request is now merged, so please update your fork and create a new branch when you resume work on it.

mmlopezu commented 8 years ago

@hlapp - will do

On Thu, Dec 17, 2015 at 9:56 PM, Hilmar Lapp notifications@github.com wrote:

@mmlopezu https://github.com/mmlopezu - note that this pull request is now merged, so please update your fork and create a new branch when you resume work on it.

— Reply to this email directly or view it on GitHub https://github.com/NESCent/popgenInfo/pull/87#issuecomment-165655582.

Margarita M. López-Uribe NSF Postdoctoral Fellow Department of Entomology and Department of Applied Ecology North Carolina State University https://sites.google.com/a/cornell.edu/mm-lopez-uribe/ https://sites.google.com/a/cornell.edu/margarita-m-lopez-uribe/