more small tweaks

Author: hpages

BBS-make-PROPAGATION_STATUS_DB.py

@@ -4,7 +4,7 @@
 ### This file is part of the BBS software (Bioconductor Build System).
 ###
 ### Author: Hervé Pagès <hpages.on.github@gmail.com>
-### Last modification: May 24, 2021
+### Last modification: Nov 22, 2023
 ###
 
 import sys
@@ -17,15 +17,20 @@
 import BBSbase
 
 def make_PROPAGATION_STATUS_DB(final_repo):
-    Rfunction = 'makePropagationStatusDb'
+    ## Prepare Rexpr (must be a single string with no spaces).
+    Rscript_path = os.path.join(BBSvars.BBS_home,
+                                'utils',
+                                'makePropagationStatusDb.R')
+    Rfun = 'makePropagationStatusDb'
     OUTGOING_dir = 'OUTGOING'
     db_filepath = 'PROPAGATION_STATUS_DB.txt'
-    script_path = os.path.join(BBSvars.BBS_home,
-                               "utils",
-                               "makePropagationStatusDb.R")
-    Rexpr = "source('%s');%s('%s','%s',db_filepath='%s')" % \
-            (script_path, Rfunction, OUTGOING_dir, final_repo, db_filepath)
+    Rfuncall = "%s('%s','%s',db_filepath='%s')" % \
+               (Rfun, OUTGOING_dir, final_repo, db_filepath)
+    Rexpr = "source('%s');%s" % (Rscript_path, Rfuncall)
+
+    ## Turn Rexpr into a system command.
     cmd = BBSbase.Rexpr2syscmd(Rexpr)
+
     try:
         ## Nasty things (that I don't really understand) can happen with
         ## subprocess.run() if this code is runned by the Task Scheduler

BBSbase.py

@@ -3,7 +3,7 @@
 ### This file is part of the BBS software (Bioconductor Build System).
 ###
 ### Author: Hervé Pagès <hpages.on.github@gmail.com>
-### Last modification: Oct 6, 2020
+### Last modification: Nov 22, 2023
 ###
 
 import sys
@@ -124,17 +124,21 @@ def extractLocalCRANstylePkgRepo(contrib_path, destdir):
     print('OK')
     return
 
-# The R expression passed thru 'Rexpr' must NOT contain spaces or it will
-# break on Windows!
+# 'Rexpr' must be a single string containing an R expression. It should NOT
+# contain spaces or it will break on Windows!
 def Rexpr2syscmd(Rexpr):
-    if BBSvars.rscript_cmd == None:
-        if sys.platform == 'win32':
+    if sys.platform == 'win32':
+        # We can't put quotes around Rexpr on Windows. This means that we
+        # can't have spaces in Rexpr.
+        if Rexpr.find(' ') >= 0:
+            sys.exit("ERROR in Rexpr2syscmd(): 'Rexpr' contains spaces!")
+        if BBSvars.rscript_cmd == None:
             syscmd = 'echo %s | %s --no-echo' % (Rexpr, BBSvars.r_cmd)
         else:
-            syscmd = 'echo "%s" | %s --no-echo' % (Rexpr, BBSvars.r_cmd)
-    else:
-        if sys.platform == 'win32':
             syscmd = '%s -e %s' % (BBSvars.rscript_cmd, Rexpr)
+    else:
+        if BBSvars.rscript_cmd == None:
+            syscmd = 'echo "%s" | %s --no-echo' % (Rexpr, BBSvars.r_cmd)
         else:
             syscmd = '%s -e "%s"' % (BBSvars.rscript_cmd, Rexpr)
     return syscmd

propagation/BBS-deploy-books.py

@@ -17,6 +17,7 @@ def _deploy_book(pkg, version, dest_dir):
     print("Deploying content from book tarball '%s' to '%s/' ..." % \
           (srcpkg_file, dest_subdir), end=' ')
     sys.stdout.flush()
+    shutil.rmtree(pkg, ignore_errors=True)  # if leftover from previous run
     if not os.path.exists(srcpkg_file):
         errmsg = "oops.. couldn't find book tarball '%s' " % srcpkg_file + \
                  "in\ndirectory:\n\n  %s\n\n" % os.getcwd() + \