`read_vcf`: `Error in file(file, "wb") : cannot open the connection`

Al-Murphy / MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

https://doi.org/doi:10.18129/B9.bioc.MungeSumstats

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`read_vcf`: `Error in file(file, "wb") : cannot open the connection` #56

Closed bschilder closed 3 years ago

bschilder commented 3 years ago

Looks like there's a line that was introduced during dev that wasn't hashed out in read_vcf: https://github.com/neurogenomics/MungeSumstats/blob/2eb54429ba71045a55d6afd534d038c8d57e3150/R/read_vcf.R#L26

save(path, nThread, temp_save, keep_extra_cols, file = "~/Downloads/temp.RData")

Was causing an error on machines without ~/Downloads folder, thus why it worked fine locally on Macs.

Removing this makes everything read in fine again.

Al-Murphy commented 3 years ago

Ah great catch, that was definitely from my debugging at an earlier stage! Hopefully that will fix the issues we were having with Bioconductor! Any chance you can push all the changes you have now so if anyone downloads MungeSumstats it will still work?

bschilder commented 3 years ago

Np, just pushed to GitHub's master branch. Tho i don't think I have push permissions to the bioconductor version of MungeSumstats, so you may have to do that step.

Al-Murphy commented 3 years ago

Pushed upstream now! Thanks for that!