Remove changes from BBS-make-OUTGOING.py and 3.20 propagation files

Author: A Wokaty

BBS-make-OUTGOING.py

@@ -11,7 +11,6 @@
 import os
 import time
 import shutil
-import subprocess
 
 import bbs.fileutils
 import bbs.parse
@@ -121,7 +120,6 @@ def copy_outgoing_pkgs(products_in_subdir, source_node):
         if BBSvars.buildtype in ['workflows', 'books', 'bioc-mac-arm64']:
             pass
         elif source_node:
-            # pdf manuals
             pdf_file = os.path.join(BBSvars.products_in_rdir.path,
                                     BBSutils.getSourceNode(),
                                     'checksrc',
@@ -134,20 +132,6 @@ def copy_outgoing_pkgs(products_in_subdir, source_node):
                 os.link(pdf_file, dst) # create hard link to avoid making a copy
             else:
                 print("BBS> [stage6b]     SKIPPED (file %s doesn't exist)" % pdf_file)
-            # html manuals
-            rel_link = "../../%s/man/%s.html"
-            hooks = f"hooks <- list(pkg_href = function(pkg) sprintf('{rel_link}', pkg, pkg));"
-            html_file = os.path.join(BBSvars.Central_rdir.path,
-                                     "OUTGOING/manuals",
-                                    '%s.html' % pkg)
-            Rexpr = hooks + f"tools::pkg2HTML('{pkg_path}',out='{html_file}',hooks=hooks)"
-            cmd = BBSbase.Rexpr2syscmd(Rexpr)
-            try:
-                print(Rexpr)
-                subprocess.run(cmd, stdout=None, stderr=subprocess.STDOUT,
-                              shell=True, check=True)
-            except subprocess.CalledProcessError as e:
-                print("BBS> [stage6b]     SKIPPED (could not generate %s)" % html_file)
     print('BBS> [stage6b] END copying outgoing packages from %s.' % srcdir)
     return
 

propagation/3.20/updateReposPkgs-bioc.sh

@@ -17,9 +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="$SRC_CONTRIB/Meta"
-META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')"
-
 if [ ! -f "$PROPAGATION_DB_FILE" ]; then
         echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?"
         exit 1
@@ -61,17 +58,6 @@ update_repo "$MAC_BIG_SUR_arm64_CONTRIB" "mac.binary.big-sur-arm64" "tgz"
 
 echo ""
 
-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', '$REPOS_ROOT', '$META_SRC'))"
-
-echo ""
-
-
 ## FIXME: Why aren't manuals propagated based on the same criteria as source
 ## packages? Looks like the former are propagated based on their timestamps
 ## only (see below) while for source packages we use the more refined
@@ -82,7 +68,7 @@ MANUALS_DEST="$REPOS_ROOT/manuals"
 MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
 echo "Updating $BIOC_VERSION/bioc repo with reference manuals..."
 for i in `ls $MANUALS_SRC`; do
-	pkg=`echo $i| awk '{split($0,a,".(html|pdf)"); print(a[1])}'`
+	pkg=`echo $i| awk '{split($0,a,".pdf"); print(a[1])}'`
 	mkdir -p $MANUALS_DEST/$pkg/man
 	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
 done

propagation/3.20/updateReposPkgs-data-annotation.sh

@@ -54,7 +54,7 @@ MANUALS_DEST="$REPOS_ROOT/manuals"
 MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
 echo "Updating $BIOC_VERSION/data/annotation repo with reference manuals..."
 for i in `ls $MANUALS_SRC`; do
-	pkg=`echo $i| awk '{split($0,a,".(html|pdf)"); print(a[1])}'`
+	pkg=`echo $i| awk '{split($0,a,".pdf"); print(a[1])}'`
 	mkdir -p $MANUALS_DEST/$pkg/man
 	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
 done

propagation/3.20/updateReposPkgs-data-experiment.sh

@@ -54,7 +54,7 @@ MANUALS_DEST="$REPOS_ROOT/manuals"
 MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
 echo "Updating $BIOC_VERSION/data/experiment repo with reference manuals..."
 for i in `ls $MANUALS_SRC`; do
-	pkg=`echo $i| awk '{split($0,a,".(html|pdf)"); print(a[1])}'`
+	pkg=`echo $i| awk '{split($0,a,".pdf"); print(a[1])}'`
 	mkdir -p $MANUALS_DEST/$pkg/man
 	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
 done