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albartcoster / pedigree

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The functions makeA and makeAinv write in a file which has a fixed name #3

Open courtiol opened 10 months ago

courtiol commented 10 months ago

The functions makeA and makeAinv write in "A.txt" and "Ainv.txt". This is dangerous as it could overwrite users files. It is also not compatible with parallel computing since different instances of R could write into the same file.

I am happy to propose a patch once issues #1 and #2 have been fixed.

A first open question is do we want "A.txt" and "Ainv.txt" to remain the default file names, or should tempfile() be the default. Using temporary files would be safer but it could break backward compatibility if other software or script assume "A.txt" or "Ainv.txt" to exist.

A second question is do we want to use files at all, as opposed to function returning data frames in R. Of course, another function could be written to write data frames onto the disk.

courtiol commented 9 months ago

NB: someone else (Serap Gonen) pointed out that blup calls makeAinv and thus that the argument passing the file must be carried over that function too.