zip_datafiles() not doing anything

[Richard Radcliffe]

Hey Karl-

I've been using R/qtl2 to map qtls in the HS/Npt, a mouse heterogeneous stock. I did some analyses a little over two years ago and all seemed to work well. Recently I've reevaluated the genotype data (from the GigaMUGA array) and have begun using these data in a new analysis with the latest version of R/qtl2.  Strangely, when I invoke the zip_datafiles() command, nothing happens. No output and no error -- just nothing. I've tried it with the old dataset that worked before and with the new one -- same result. Any ideas? Below is the command I used and the yaml file.

>zip_datafiles("control_47593.yaml")

# YAML format

# This is the R/QTL2 control file for data files related to the Nicotine preference project. 

# Population = HS/Npt

# Genotypes derived from the GigaMUGA array

crosstype: hs

geno: geno_47593.csv

geno_transposed: true

founder_geno: npt_geno_47593.csv

founder_geno_transposed: true

genotypes:

  A: 1

  H: 2

  B: 3

pheno: pheno_476_corrected.csv

pheno_transposed: false

covar: covar_476_corrected.csv

sex:

  covar: sex

  f: female

  m: male

x_chr: X

cross_info: 

  covar: ngen

gmap: gmap_47593.csv

pmap: pmap_47593.csv

alleles: 

- A

- B

- C

- D

- E

- F

- G

- H

na.strings: 

- NA

- ‘-‘

[Karl Broman]

What operating system are you using? And what version of R and R/qtl2.

Type R.version and qtl2::qtl2version().

If zip_datafiles() works, it won't produce any output but will create a zip file where that .yaml file is located.

It's not a very critical function; you could just go to that directory and zip the files directly yourself, but I'm surprised it's not working without giving some error message.

Maybe if you use quiet=FALSE when you call zip_datafiles(), it'll give some message about what's going wrong?

karl

[Richard Radcliffe]

Windows 10

Rstudio 1.4.1103

R 4.0.3

qtl2 0.24

The quiet=FALSE did not produce any messages or any other kind of output. I always assumed zip_datafiles() did something in addition to, you know, zip the datafiles (doh!), so from that perspective, my immediate problem is solved. However, if you'd like to track down whatever is going on, I'm happy to help any way I can.  

-Richard