Linux and macOS use MulticoreParam() by default, and the 'workers' inherit the
environment (e.g., loaded packages) of the 'manager'. Windows doesn't support
this mode, and instead uses SnowParam() by default; likely you'll be able to
reproduce the error on your system by using SnowParam(), perhaps via
register(SnowParam()) or explicitly in your function.
Likely, your function assumes that it has access to a variable defined in the
global environment; this should be made explicit by passing that variable as an
argument. Here's an illustration of the principle (not exactly your error)
> m = matrix(0, 26, 26, dimnames = list(letters, LETTERS))
> library(BiocParallel)
> bplapply(1:3, function(...) rownames(m), BPPARAM = MulticoreParam(2))
[[1]]
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[20] "t" "u" "v" "w" "x" "y" "z"
[[2]]
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[20] "t" "u" "v" "w" "x" "y" "z"
[[3]]
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[20] "t" "u" "v" "w" "x" "y" "z"
> bplapply(1:3, function(...) rownames(m), BPPARAM = SnowParam(2))
Error: BiocParallel errors
2 remote errors, element index: 1, 2
1 unevaluated and other errors
first remote error:
Error in rownames(m): object 'm' not found
and the solution (by passing 'm' explicitly to the function)
> bplapply(1:3, function(..., m) rownames(m), m = m, BPPARAM = SnowParam(2))
[[1]]
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[20] "t" "u" "v" "w" "x" "y" "z"
[[2]]
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[20] "t" "u" "v" "w" "x" "y" "z"
[[3]]
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[20] "t" "u" "v" "w" "x" "y" "z"
Martin
On 11/22/21, 12:15 PM, "Bioc-devel on behalf of Daniel, Dimitrov"
<bioc-devel-boun...@r-project.org on behalf of
daniel.dimit...@uni-heidelberg.de> wrote:
Dear BioConductor developers,
Two windows users of a package that I'm developing (soon to be submitted
to BioC) have encountered the same error
<https://github.com/saezlab/liana/issues/25>:
```
Error: BiocParallel errors
� element index: 1, 2, 3
� first error: invalid length of row names
```
This error is not reproducible in either Mac, nor Linux, and from my
search I could pin point it to differences in which variables from the
parent environment are handled on Windows.
The package that seems to be throwing this error is *scuttle*, and in
particular the summarizeAssayByGroup function's call to BiocParallel.
Any help would be appreciated.
Kindest regards,
Daniel Dimitrov
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