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transform_sample_counts() fails on multi-argument functions #1262

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mikemc opened this issue Nov 8, 2019 · 0 comments · May be fixed by #1263
Open

transform_sample_counts() fails on multi-argument functions #1262

mikemc opened this issue Nov 8, 2019 · 0 comments · May be fixed by #1263

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@mikemc
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mikemc commented Nov 8, 2019 

library(phyloseq)
data(GlobalPatterns)

f <- function(x, y) {x + y}
ps <- transform_sample_counts(GlobalPatterns, f, y = 2)
#> Error in fun(1:10): argument "y" is missing, with no default

Created on 2019-11-08 by the reprex package (v0.3.0)

The problem is due to a missing ... at

phyloseq/R/transform_filter-methods.R

Line 817 in 3fb790f

if( !identical(length(fun(1:10)), 10L) ){stop("`fun` not valid function.")}

Changing this line to

	if( !identical(length(fun(1:10, ...)), 10L) ){stop("`fun` not valid function.")}

fixes the issue.
mikemc added a commit to mikemc/phyloseq that referenced this issue Nov 8, 2019
@mikemc
Fix bug in transform_sample_counts()
d38e7e4 
Fixes joey711#1262
@mikemc mikemc linked a pull request Nov 8, 2019 that will close this issue
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Fix bug in transform_sample_counts() mikemc/phyloseq
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@mikemc