enrichPathway error when checking condition lengths used
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@lluis-revilla-sancho
Last seen 3 days ago
European Union

In my user .Renviron I have set two variables to check correctness of code:

_R_CHECK_LENGTH_1_CONDITION_ =${_R_CHECK_LENGTH_1_CONDITION_-verbose}
_R_CHECK_LENGTH_1_LOGIC2_=${_R_CHECK_LENGTH_1_LOGIC2_-verbose}

This variables trigger an error report when using ReatcomePA:enrichPathway example code:

gene <- c("11171", "8243", "112464", "2194",
            "9318", "79026", "1654", "65003",
            "6240", "3476", "6238", "3836",
            "4176", "1017", "249")
yy = enrichPathway(gene, pvalueCutoff=0.05)

See the last lines of the error

<environment: namespace:DOSE>
 --- function search by body ---
Function TERM2NAME in namespace DOSE has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in is.null(PATHID2NAME) || is.na(PATHID2NAME) : 
  'length(x) = 2257 > 1' in coercion to 'logical(1)'

This is in R version 3.6.3 and Bioconductor version 3.10

DOSE ReactomePA • 237 views
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