def makeNodeInfo():
# Generate the NodeInfo files (the files containing some node related info)
NodeInfo_subdir = "NodeInfo"
print "BBS> Updating BBS_WORK_TOPDIR/%s" % NodeInfo_subdir
NodeInfo_path = os.path.join(BBSvars.work_topdir, NodeInfo_subdir)
bbs.fileutils.remake_dir(NodeInfo_path)
os.chdir(NodeInfo_path)
writeRversion()
writeRconfig()
Rscript = "sessionInfo()"
bbs.jobs.runJob(BBSbase.Rscript2syscmd(Rscript), \
'R-sessionInfo.txt', 60.0, True) # ignore retcode
Rscript = "data.frame(installed.packages()[,c('Version','Built')])"
bbs.jobs.runJob(BBSbase.Rscript2syscmd(Rscript), \
'R-instpkgs.txt', 60.0, True) # ignore retcode
writeSysCommandVersion('CC')
writeSysCommandVersion('CXX')
writeSysCommandVersion('CXX98')
writeSysCommandVersion('CXX11')
writeSysCommandVersion('CXX14')
writeSysCommandVersion('F77')
writeSysCommandVersion('FC')
print "BBS> cd BBS_WORK_TOPDIR"
os.chdir(BBSvars.work_topdir)
BBSvars.Node_rdir.Put(NodeInfo_subdir, True, True)
return
def make_STAGE2_pkg_deps_list(target_pkgs):
# Make 'target_pkgs.txt' file.
target_pkgs_file = "target_pkgs.txt"
out = open(target_pkgs_file, 'w')
for pkg in target_pkgs:
out.write("%s\n" % pkg)
out.close()
print "BBS> [make_STAGE2_pkg_deps_list]",
print "%s pkgs written to %s" % (len(target_pkgs), target_pkgs_file)
# Make 'STAGE2_pkg_deps_list.txt' file.
Rfunction = "make_STAGE2_pkg_deps_list"
script_path = os.path.join(BBScorevars.BBS_home,
"utils",
"make_STAGE2_pkg_deps_list.R")
STAGE2_pkg_deps_list_path = "STAGE2_pkg_deps_list.txt"
print "BBS> [make_STAGE2_pkg_deps_list]",
print "Calling %s() defined in %s to make %s file ..." % \
(Rfunction, script_path, STAGE2_pkg_deps_list_path),
# Backslashes in the paths injected in 'Rscript' will be seen as escape
# characters by R so we need to replace them. Nothing will be replaced
# on a Unix-like platform, only on Windows where the paths can actually
# contain backslashes.
script_path2 = script_path.replace('\\', '/')
target_pkgs_file2 = target_pkgs_file.replace('\\', '/')
STAGE2_pkg_deps_list_path2 = STAGE2_pkg_deps_list_path.replace('\\', '/')
# Use short.list=TRUE to skip installation of target packages not needed
# by another target package for build or check.
#Rscript = "source('%s');%s('%s',outfile='%s',short.list=TRUE)" % \
Rscript = "source('%s');%s('%s',outfile='%s')" % \
(script_path2, Rfunction, target_pkgs_file2,
STAGE2_pkg_deps_list_path2)
out_file = Rfunction + ".Rout"
bbs.jobs.runJob(BBSbase.Rscript2syscmd(Rscript), out_file) # ignore retcode
print "OK"
# Load 'STAGE2_pkg_deps_list.txt' file.
print "BBS> [make_STAGE2_pkg_deps_list] Loading %s file ..." % \
STAGE2_pkg_deps_list_path,
f = open(STAGE2_pkg_deps_list_path, 'r')
pkg_deps_list = {}
EMPTY_STRING = ''
for line in f:
(pkg, deps) = line.split(":")
deps = deps.strip().split(" ")
if EMPTY_STRING in deps:
deps.remove(EMPTY_STRING)
pkg_deps_list[pkg] = deps
f.close()
print "OK (%s pkgs and their deps loaded)" % len(pkg_deps_list)
print "BBS> [make_STAGE2_pkg_deps_list] DONE."
return pkg_deps_list
def get_installed_pkgs():
installed_pkgs_path = "installed_pkgs.txt"
Rscript = "writeLines(rownames(installed.packages()),'%s')" % \
installed_pkgs_path
out_file = "get_installed_pkgs.Rout"
bbs.jobs.runJob(BBSbase.Rscript2syscmd(Rscript), out_file) # ignore retcode
installed_pkgs = []
f = open(installed_pkgs_path, 'r')
for line in f:
installed_pkgs.append(line.strip())
f.close()
print "BBS> [get_installed_pkgs] %s installed pkgs" % len(installed_pkgs)
return installed_pkgs
def CallRfunctionFromSTAGE2Script(Rfunction, out_file=None):
print "BBS> [%s] BEGIN ..." % Rfunction
script_path = BBSvars.STAGE2_r_script
# Backslahes in the paths injected in 'Rscript' will be seen as escape
# characters by R so we need to replace them. Nothing will be replaced
# on a Unix-like platform, only on Windows where the paths can actually
# contain backslahes.
script_path = script_path.replace('\\', '/')
Rscript = "source('%s');%s()" % (script_path, Rfunction)
if out_file == None:
out_file = '%s.Rout' % Rfunction
bbs.jobs.runJob(BBSbase.Rscript2syscmd(Rscript), out_file, 3600.0) # ignore retcode
print "BBS> [%s] END." % Rfunction
return
