diff --git a/propagation/3.22/updateReposPkgs-bioc.sh b/propagation/3.22/updateReposPkgs-bioc.sh index 60b65810..ba4aeccd 100755 --- a/propagation/3.22/updateReposPkgs-bioc.sh +++ b/propagation/3.22/updateReposPkgs-bioc.sh @@ -17,10 +17,6 @@ WIN_CONTRIB="$REPOS_ROOT/bin/windows/contrib/$R_VERSION" MAC_BIG_SUR_x86_64_CONTRIB="$REPOS_ROOT/bin/macosx/big-sur-x86_64/contrib/$R_VERSION" MAC_BIG_SUR_arm64_CONTRIB="$REPOS_ROOT/bin/macosx/big-sur-arm64/contrib/$R_VERSION" -META_SRC="$SRC_CONTRIB/Meta" -META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')" -MEAT_PATH="/home/biocbuild/bbs-$BIOC_VERSION-bioc/meat" - if [ ! -f "$PROPAGATION_DB_FILE" ]; then echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?" exit 1 @@ -76,13 +72,6 @@ for i in `ls $MANUALS_SRC`; do mkdir -p $MANUALS_DEST/$pkg/man cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man done -echo "" -echo "========================================================================" -/bin/date -echo "------------------------------------------------------------------------" - -echo "Updating $META_SRC with aliases and cross refences dbs..." -$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$MEAT_PATH', '$REPOS_ROOT', '$META_SRC'))" echo "DONE." exit 0 diff --git a/propagation/3.22/updateReposPkgs-data-annotation.sh b/propagation/3.22/updateReposPkgs-data-annotation.sh index 01bd5b6a..da8d1316 100755 --- a/propagation/3.22/updateReposPkgs-data-annotation.sh +++ b/propagation/3.22/updateReposPkgs-data-annotation.sh @@ -14,10 +14,6 @@ PROPAGATION_DB_FILE="$BBS_OUTGOING_DIR/../PROPAGATION_STATUS_DB.txt" REPOS_ROOT="$HOME/PACKAGES/$BIOC_VERSION/data/annotation" SRC_CONTRIB="$REPOS_ROOT/src/contrib" -META_SRC="$SRC_CONTRIB/Meta" -META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')" -MEAT_PATH="/home/biocbuild/bbs-$BIOC_VERSION-data-annotation/meat" - if [ ! -f "$PROPAGATION_DB_FILE" ]; then echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?" exit 1 @@ -62,13 +58,6 @@ for i in `ls $MANUALS_SRC`; do mkdir -p $MANUALS_DEST/$pkg/man cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man done -echo "" -echo "========================================================================" -/bin/date -echo "------------------------------------------------------------------------" - -echo "Updating $META_SRC with aliases and cross refences dbs..." -$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$MEAT_PATH', '$REPOS_ROOT', '$META_SRC'))" echo "DONE." exit 0 diff --git a/propagation/3.22/updateReposPkgs-data-experiment.sh b/propagation/3.22/updateReposPkgs-data-experiment.sh index 35ba19e6..ffaa53ab 100755 --- a/propagation/3.22/updateReposPkgs-data-experiment.sh +++ b/propagation/3.22/updateReposPkgs-data-experiment.sh @@ -14,10 +14,6 @@ PROPAGATION_DB_FILE="$BBS_OUTGOING_DIR/../PROPAGATION_STATUS_DB.txt" REPOS_ROOT="$HOME/PACKAGES/$BIOC_VERSION/data/experiment" SRC_CONTRIB="$REPOS_ROOT/src/contrib" -META_SRC="$SRC_CONTRIB/Meta" -META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')" -MEAT_PATH="/home/biocbuild/bbs-$BIOC_VERSION-data-experiment/meat" - if [ ! -f "$PROPAGATION_DB_FILE" ]; then echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?" exit 1 @@ -62,13 +58,6 @@ for i in `ls $MANUALS_SRC`; do mkdir -p $MANUALS_DEST/$pkg/man cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man done -echo "" -echo "========================================================================" -/bin/date -echo "------------------------------------------------------------------------" - -echo "Updating $META_SRC with aliases and cross refences dbs..." -$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$MEAT_PATH', '$REPOS_ROOT', '$META_SRC'))" echo "DONE." exit 0 diff --git a/utils/makeMetaDbs.R b/utils/makeMetaDbs.R deleted file mode 100644 index ec0926a1..00000000 --- a/utils/makeMetaDbs.R +++ /dev/null @@ -1,33 +0,0 @@ -makeMetaDbs <- function(db_filepath, repos_root, meta_path) { - - meat_dir <- Sys.getenv("BBS_MEAT_PATH") - prop_status <- read.dcf(db_filepath) - - pkgs <- c() - for (i in 1:dim(prop_status)[2]) { - pkg_type_stage <- strsplit(colnames(prop_status)[i], "#")[[1]] - if ("source" %in% pkg_type_stage && - strsplit(prop_status[i], ",")[[1]][1] %in% c("YES", "UNNEEDED")) { - pkgs <- c(pkgs, pkg_type_stage[1]) - } - } - - web_dir <- file.path(repos_root, "web", "packages") - meta_dir <- file.path(meta_path) - if (!dir.exists(meta_dir)) { - dir.create(meta_dir, recursive = TRUE) - } - - pkg_paths <- file.path(meat_dir, pkgs) - for (pkg_path in pkg_paths) { - biocViews::build_db_from_source(pkg_path, repos_root) - } - - aliases_db_file <- file.path(meta_dir, "aliases.rds") - meta_aliases_db <- biocViews::build_meta_aliases_db(web_dir, aliases_db_file) - saveRDS(meta_aliases_db, aliases_db_file, version = 2) - - rdxrefs_db_file <- file.path(meta_dir, "rdxrefs.rds") - meta_rdxrefs_db <- biocViews::build_meta_rdxrefs_db(web_dir, rdxrefs_db_file) - saveRDS(meta_rdxrefs_db, rdxrefs_db_file, version = 2) -}