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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