This is again a repetition of the same problem, but I was forced to put it as new question. So please donot delete this admins!
I am new to R and Rpy2. My problem is similar. I am using p*ython 2.6, R 2.15.1, rpy2 2.2.6, and Windows 7*.
R_HOME: C:\Program Files\R\R-2.15.1
Typing "R" in the command prompt does not work.
PATH: has these two--C:\Program Files\R\R-2.15.1\bin;C:\Program Files\R\R-2.15.1
PYTHONPATH: C:\Python26\ArcGIS10.0\Lib;C:\Python26\ArcGIS10.0\DLLs;C:\Python26\ArcGIS10.0\Lib\lib-tk
When I run the setup.py I get "error: no commands supplied"!
I tried putting all file from bin/i386 to directly under bin.
My rinterface->init.py is different. However this is what I did:
# MSWindows-specific code
_win_ok = False
if sys.platform in _win_bindirs.keys():
import win32api
if os.path.exists(os.path.join(R_HOME, 'lib')): ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'bin')
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'modules')
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'lib')
R_DLL_DIRS = ('bin', 'lib')
else: ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'bin', 'i386') ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'modules', 'i386') ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'library') ## ADDED ##
R_DLL_DIRS = ('bin', 'library')
# Load the R dll using the explicit path
# Try dirs in R_DLL_DIRS
for r_dir in R_DLL_DIRS:
Rlib = os.path.join(R_HOME, r_dir, _win_bindirs[sys.platform], 'R.dll')
if not os.path.exists(Rlib):
continue
win32api.LoadLibrary(Rlib)
_win_ok = True
break
# Otherwise fail out!
if not _win_ok:
raise RuntimeError("Unable to locate R.dll within %s" % R_HOME)
# cleanup the namespace
del(os)
Nothing changes the setup.py error message. I am at my wits end. Please help!!
Avishek
Check the rpy mailing-list entries for the last week or so. There is a contributed binary built.
Related
When I run sqlplus in Python using subprocess I get no output when there are SQL errors, or update or insert statements returning number of rows updated or inserted. When I run select statements with no errors I do get the output.
Here is my code:
This creates a string with newlines that are then written to process.stdin.write()
def write_sql_string(process, args):
sql_commands = ''
sql_commands += "WHENEVER SQLERROR EXIT SQL.SQLCODE;\n"
sql_line = '#' + args.sql_file_name
if crs_debug:
print('DEBUG: ' + 'sys.argv', ' '.join(sys.argv))
if len(args.sql_args) > 0:
len_argv = len(args.sql_args)
sql_commands += "SET VERIFY OFF\n"
for i in range(0, len_argv):
sql_line += ' "' + args.sql_args[i] + '"'
sql_commands += sql_line + "\n"
# if prod_env:
sql_commands += "exit;\n"
if crs_debug:
print('DEBUG: ' + 'sql_line: ' + sql_line)
process.stdin.write(sql_commands)
This code executes the SQL commands
def execute_sql_file(username, dbpass, args):
db_conn_str = username + '/' + dbpass + '#' + args.dbname
# '-S', - Silent
sqlplus_cmd = ['sqlplus', '-S', '-L', db_conn_str]
if crs_debug:
print('DEBUG: ' + ' '.join(sqlplus_cmd))
process = subprocess.Popen(sqlplus_cmd,
stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
write_sql_string(process, args)
stdout, stderr = process.communicate()
# Get return code of sql query
stdout_lines = stdout.split("\n")
print('STDOUT')
for line in stdout_lines:
line = line.rstrip()
print(line)
stderr_lines = stderr.split("\n")
print('STDERR')
for line in stderr_lines:
line = line.rstrip()
print(line)
sqlplus_rc = process.poll()
# Check if sqlplus returned an error
if sqlplus_rc != 0:
print("FAILURE in " + script_name + " in connecting to Oracle exit code: " + str(sqlplus_rc))
print(stderr_data)
sys.exit(sqlplus_rc)
When I run I run my code for a SQL file that requires parameters, if I run it with missing parameters I get no output. If I run it with parameters I get the correct output.
Here is an example SQL file sel_dual.sql:
SELECT 'THIS IS TEXT &1 &2' FROM dual;
As an example command line:
run_sql_file.py dbname sql_file [arg1]...[argn]
If I run the script with
run_sql_file.py dbname sel_dual.py
I get no output, even though it should ask for a parameter and give other error output.
If I run the script with
run_sql_file.py dbname sel_dual.py Seth F
I get the proper output:
'THISISTEXTSETHF'
----------------------------------------------------------------------------
THIS IS TEXT Seth F
The args referred to is the result of processing args with the argparse module:
parser = argparse.ArgumentParser(description='Run a SQL file with ptional arguments using SQLPlus')
parser.add_argument('dbname', help='db (environment) name')
parser.add_argument('sql_file_name', help='sql file')
parser.add_argument('sql_args', nargs='*', help='arguments for sql file')
args = parser.parse_args()
Does anybody know what could be causing this? I've omitted the rest of the script since it basically gets command arguments and validates that the SQL file exists.
I am running sqlplus version Release 12.1.0.2.0 Production. I am running Python version 3.7.6. I am running on Linux (not sure what version). The kernel release is 4.1.12-124.28.5.el7uek.x86_64.
I am trying to format output from the following Python 3.x script. Here is the function that I'm calling:
def daily_backup():
# Header for /var/log/me/rsync_backup.log
print(" ")
print("#" * 75)
print(get_dt())
print("#" * 75)
print(" ")
# Update timestamp on backup file, notify user that backup has started
Path("/var/log/me/rsync_backup_ran").touch()
notify_send("Daily backup started","%s" % get_dt(),"info")
# Every week, start over with current files
if today_name != "Sunday":
rsync_command = "rsync -avbH --stats --exclude-from=/home/me/bin/rsync_backup.ecl"
else:
rsync_command = "rsync -avH --stats --exclude-from=/home/me/bin/rsync_backup.ecl " \
"--delete --delete-excluded"
# System configs, crontabs, installed software lists
INSTALLED = "/home/me/.config/installed"
if not os.path.isdir(INSTALLED):
os.mkdir(INSTALLED)
os.system("dpkg --get-selections > %s/installed-software" % INSTALLED)
os.system("ls /home/me/.local/share/flatpak/app > %s/installed-flatpaks" % INSTALLED)
os.system("rsync -avb /etc/apt/sources.list.d %s" % INSTALLED)
os.system("rsync -avb /var/spool/cron %s" % INSTALLED)
os.system("rsync -avb /etc/libvirt/qemu %s" % INSTALLED)
# My data
for i in range(3):
cmd_format = "%s %s %s/%s/daily"
cmd_info = (rsync_command, backup_paths[i], backup_root, backup_folders[i])
os.system(cmd_format % cmd_info)
notify_send("Daily backup ended","%s" % get_dt(),"info")
daily_backup()
The script works, except for that the header I create (at the top of the function) doesn't get printed until after all of the os.system calls. Is this normal behavior? How can I correct this?
It's probably a problem with the stdout.
Try to force it following this SO previous post
I am creating a tool that gives an overview of hundredths of test results. This tool access a log file, checks for Pass and Fail verdicts. When it is a fail, I need to go back to previous lines of the log to capture the cause of failure.
The linecache.getline works in my workspace (Python Run via eclipse). But after I created a windows installer (.exe file) and installed the application in my computer, the linecache.getline returns nothing. Is there something I need to add into my setup.py file to fix this or is it my code issue?
Tool Code
precon:
from wx.FileDialog, access the log file
self.result_path = dlg.GetPath()
try:
with open(self.result_path, 'r') as file:
self.checkLog(self.result_path, file)
def checkLog(self, path, f):
line_no = 1
index = 0
for line in f:
n = re.search("FAIL", line, re.IGNORECASE) or re.search("PASS", line, re.IGNORECASE)
if n:
currentline = re.sub('\s+', ' ', line.rstrip())
finalresult = currentline
self.list_ctrl.InsertStringItem(index, finaltestname)
self.list_ctrl.SetStringItem(index, 1, finalresult)
if currentline == "FAIL":
fail_line1 = linecache.getline(path, int(line_no - 3)) #Get reason of failure
fail_line2 = linecache.getline(path, int(line_no - 2)) #Get reason of failure
cause = fail_line1.strip() + " " + fail_line2.strip()
self.list_ctrl.SetStringItem(index, 2, cause)
index += 1
line_no += 1
The issue was resolved by doing the get_line function from this link:
Python: linecache not working as expected?
I've encountered a problem trying to set up a C++ project on my Mac (Yosemite with Xcode 6) using CMake with Unix style Makefiles and vim with the youcompleteme plugin (I'm a Linux veteran and Mac newbie so I prefer this setup to Xcode). The code builds and runs but youcompleteme throws some bogus errors which I think boil down to it not being able to find the <cstdint> header.
I've just tried it on Linux too, and had the same problem.
I've configured .ycm_extra_conf.py to use a compile_commands.json generated by cake. The "command" lines in compile_commands.json use these flags:
"command": "/usr/bin/c++ -std=c++11 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks -I/usr/local/include -I/Users/tony/Dev/cow/jni -I/Users/tony/Library/Frameworks/SDL2.framework/Headers -Wall -Wextra -Wunused -F/Users/tony/Library/Frameworks -o ...
There doesn't seem to be an explicit reference there to any directory containing stdint as a direct parent.
Is there a way I can get youcompleteme to do its stuff with libclang in such a way that it can find the directory implicitly, which seems to work when running c++ on the command line? Or what's the best way to get cmake to add an appropriate system header path without hardwiring it? I want my CMakeLists.txt to be portable and to be able to cope with toolchain upgrades.
My .ycm_extra_conf.py was pretty much a copy of the supplied example modified slightly to find compile_commands.json where I put it.
As #ladislas said, YCM needs to be explicitly pointed to all relevant include directories as libclang won't use the same implicit location a normal compiler driver invocation (i.e. clang++ from the command line) would use.
What I usually do, on OSX, is to let YCM know about Xcode's libc++ headers with something like (in .ycm_extra_conf.py):
import os
import ycm_core
import subprocess
xcode_cpp11headers = subprocess.Popen("xcode-select -p", stdout = subprocess.PIPE, shell=True).communicate()[0].rstrip('\n') + '/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1'
.
.
flags = [
.
.
'-isystem',
xcode_cpp11headers,
.
.
]
The "xcode_cpp11headers" variable is populated with the proper path depending on the location of your current Xcode's installation, and you can change it accordingly if you want to use say the commandline-tools version of libc++ (i.e. the includes are in /Library/Developer/CommandLineTools/usr/include/c++/v1) or a source distribution of libc++ if you have compiled your own.
Of course this is platform dependant and either you provide a platform specific .ycm_extra_conf.py alongside your project, or you can populate that variable differently with some extra python code accordingly to the current platform.
You must add all the paths where YCM needs to look for your sources, libraries, and so on.
It does not work recursively, so it's a little bit cumbersome at first but is should not change once set for your project.
As an example, here is mine for an Arduino project :
https://github.com/ladislas/Bare-Arduino-Project/blob/master/.ycm_extra_conf.py#L21
Hope this helps!
EDIT - 2015/01/08
The solution of #abigagli is very elegant! I too use something like this to parse my lib directory and look for .h files to add their path to flags.
Here it is if it can be useful :) http://git.io/IiR1JA
As I found out from the above answers, YCM needs to be told the compiler's system include paths which are usually implicit in other ways of using the compiler. I added a function GetSystemIncludePaths() to .ycm_extra_conf.py to discover and cache these paths portably. Here's the full file with comments and irrelevant content of flags list snipped. The original is Copyright (C) 2014 Google Inc with a GPL2+ licence:
import subprocess, os
import ycm_core
flags = []
def DirectoryOfThisScript():
return os.path.dirname( os.path.abspath( __file__ ) )
compilation_database_folder = os.path.abspath(
os.path.join(DirectoryOfThisScript(), 'build-make'))
if os.path.exists( compilation_database_folder ):
database = ycm_core.CompilationDatabase( compilation_database_folder )
else:
database = None
SOURCE_EXTENSIONS = [ '.cpp', '.cxx', '.cc', '.c', '.m', '.mm' ]
def MakeRelativePathsInFlagsAbsolute( flags, working_directory ):
if not working_directory:
return list( flags )
new_flags = []
make_next_absolute = False
path_flags = [ '-isystem', '-I', '-iquote', '--sysroot=' ]
for flag in flags:
new_flag = flag
if make_next_absolute:
make_next_absolute = False
if not flag.startswith( '/' ):
new_flag = os.path.join( working_directory, flag )
for path_flag in path_flags:
if flag == path_flag:
make_next_absolute = True
break
if flag.startswith( path_flag ):
path = flag[ len( path_flag ): ]
new_flag = path_flag + os.path.join( working_directory, path )
break
if new_flag:
new_flags.append( new_flag )
return new_flags
def IsHeaderFile( filename ):
extension = os.path.splitext( filename )[ 1 ]
return extension in [ '.h', '.hxx', '.hpp', '.hh' ]
def GetCompilationInfoForFile( filename ):
if IsHeaderFile( filename ):
basename = os.path.splitext( filename )[ 0 ]
for extension in SOURCE_EXTENSIONS:
replacement_file = basename + extension
if os.path.exists( replacement_file ):
compilation_info = database.GetCompilationInfoForFile(
replacement_file )
if compilation_info.compiler_flags_:
return compilation_info
return None
return database.GetCompilationInfoForFile( filename )
def GetSystemIncludePaths():
cache = os.path.join(DirectoryOfThisScript(), ".ycm_sys_incs")
if os.path.exists(cache):
fp = open(cache, 'r')
flags = fp.readlines()
fp.close()
flags = [s.strip() for s in flags]
else:
devnull = open(os.devnull, 'r')
child = subprocess.Popen(["/usr/bin/cpp", "-xc++", "-v"],
stdin = devnull, stderr = subprocess.PIPE)
output = child.communicate()[1].split('\n')
devnull.close()
flags = []
status = 0
for l in output:
l = l.strip()
if l == '#include "..." search starts here:':
status = 1
elif l == '#include <...> search starts here:':
status = 2
elif status:
if l == 'End of search list.':
break
elif l.endswith('(framework directory)'):
continue
elif status == 1:
flags.append('-I')
elif status == 2:
flags.append('-isystem')
flags.append(os.path.normpath(l))
fp = open(cache, 'w')
fp.write('\n'.join(flags))
fp.close()
return flags
def FlagsForFile( filename, **kwargs ):
if database:
compilation_info = GetCompilationInfoForFile( filename )
if not compilation_info:
return None
final_flags = MakeRelativePathsInFlagsAbsolute(
compilation_info.compiler_flags_,
compilation_info.compiler_working_dir_ )
sys_incs = GetSystemIncludePaths()
if sys_incs:
final_flags += sys_incs
else:
relative_to = DirectoryOfThisScript()
final_flags = MakeRelativePathsInFlagsAbsolute( flags, relative_to )
return {
'flags': final_flags,
'do_cache': True
}
Setup is following:
Apache with WSGI successfully set up and running on bare bones application
import sys
# Path of the directory where scripts directory is located.
sys.path.insert(0, 'C:\\Users\\xxx\\Documents\\Programming\\www\\scripts')
from Blog import Blog #Blog.py is a file in the scripts directory
def application(environ, start_response):
status = '200 OK'
output = ''
b = Blog()
for key in environ.keys():
output = output + str(key) + ' : ' + str(environ[key]) + '<br/>'
output = "Test: " + b.title + "<br/>" + b.text + "<br/>" + output
output = b.get_blog() + "<br/>" + output
response_headers = [('Content-type', 'text/html'),
('Content-Length', str(len(output)))]
start_response(status, response_headers)
return [output]
the relevant parts of Blog.py looks like this
class Blog:
#blogid is a str
def get_blog(self):
conn = sqlite3.connect(self.database)
c = conn.cursor()
# get the blog
c.execute('select * from blogs')
results = []
for row in c:
results.append(row)
c.close()
return results
Apache error log gives me:
line 21, in application
output = b.get_blog() + "<br/>" + output
AttributeError: Blog instance has no attribute 'get_blog'
Changing the b.get_blog to str(dir(b)) gives me:
['doc', 'init', 'module', 'get_data', 'text', 'title'] which is an old version of the Blog class, one that I included in the wsgi file a while ago. I can't find where it's being cached or then why it's not being over written by the Blog import because if I change the import to just import Blog and the instantiation to Blog.Blog() it still gives the same dir contents.
Imported modules have an '__file__' attribute. Print that out, it will tell you where the file is that it loaded for the module. Then you can work out the conflict.
Maybe a version elsewhere on module search path or could be an old .pyc file.