From e6d49755994bec3878bc0b3ec70ec1ae4e894fe7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= Date: Wed, 30 Oct 2019 13:55:31 -0700 Subject: [PATCH] Small tweak to createPropagationDB.R to work around issue in BiocManager https://github.com/Bioconductor/BiocManager/issues/46#issuecomment-548017624 --- utils/createPropagationDB.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/utils/createPropagationDB.R b/utils/createPropagationDB.R index c98e7307..c5254974 100644 --- a/utils/createPropagationDB.R +++ b/utils/createPropagationDB.R @@ -19,8 +19,10 @@ library(tools) rvers <- paste(getRversion()$major, getRversion()$minor, sep=".") + biocvers <- BiocManager::version() +biocrepos <- BiocManager:::.repositories(character(), version=biocvers) # Takes as input the value of an Imports, Depends, # or LinkingTo field and returns a named character @@ -328,7 +330,7 @@ createPropagationList <- function(outgoingDirPath, propagationDbFilePath, "data/experiment" = "BioCexp", "workflows" = "BioCworkflows") bioc.apdb <<- available.packages( - contrib.url(BiocManager::repositories()[[repo.name]]), + contrib.url(biocrepos[[repo.name]]), type="source") bioc.apdf <<- as.data.frame(bioc.apdb, stringsAsFactors=FALSE) bioc.ap <<- rownames(bioc.apdb)