I have a Julia program that inputs a csv and transforms the data via a bunch of functions, and outputs a csv file. I want to turn this into a binary so that I can run on different machines without having the source code on different machines.
I am looking at PackageCompiler.jl, but I can't find any understandable documentation for creating a binary app. I am trying:
using PackageCompiler
#time create_app("JuliaPrograms", "test"; precompile_execution_file="script.jl")
The file that contains all my code is script.jl and it lives in the dir JuliaPrograms, and I want the compiled binary to be named test.
When I run julia script.jl it performs as I want. I want to be able to run ./test with the same result.
However, I get this error:
ERROR: could not find project at "/Users/userx/JuliaPrograms/"
What am I doing wrong? Do I need some special project directory?
Per the docs here: https://julialang.github.io/PackageCompiler.jl/dev/apps.html#Creating-an-app-1 you need to make sure you define:
function julia_main()::Cint
# do something based on ARGS?
return 0 # if things finished successfully
end
a function called julia_main as the entry point to the app. You can find an example app here: https://github.com/JuliaLang/PackageCompiler.jl/tree/master/examples/MyApp
You may also want to check the location of the code itself. Is it being saved at "/Users/userx/JuliaPrograms/"? You can switch your directory in the Julia Reply by typing ; which will enter you into shell mode and then you can cd into the directory where your code is.
Related
I'm trying to use Atom to run a Lua script. However, when I try to load files via the require() command, it always says it's unable to locate them. The files are all in the same folder. For example, to load utils.lua I have tried
require 'utils'
require 'utils.lua'
require 'D:\Users\Mike\Dropbox\Lua Modeling\utils.lua'
require 'D:\\Users\\Mike\\Dropbox\\Lua Modeling\\utils.lua'
require 'D:/Users/Mike/Dropbox/Lua Modeling/utils.lua'
I get errors like
Lua: D:\Users\Mike\Dropbox\Lua Modeling\main.lua:12: module 'D:\Users\Mike\Dropbox\Lua Modeling\utils.lua' not found:
no field package.preload['D:\Users\Mike\Dropbox\Lua Modeling\utils.lua']
no file '.\D:\Users\Mike\Dropbox\Lua Modeling\utils\lua.lua'
no file 'D:\Program Files (x86)\Lua\5.1\lua\D:\Users\Mike\Dropbox\Lua Modeling\utils\lua.lua'
no file 'D:\Program Files (x86)\Lua\5.1\lua\D:\Users\Mike\Dropbox\Lua Modeling\utils\lua\init.lua'
no file 'D:\Program Files (x86)\Lua\5.1\D:\Users\Mike\Dropbox\Lua Modeling\utils\lua.lua'
The messages says on the first line that 'D:\Users\Mike\Dropbox\Lua Modeling\utils.lua' was not found, even though that is the full path of the file. What am I doing wrong?
Thanks.
The short answer
You should be able to load utils.lua by using the following code:
require("utils")
And by starting your program from the directory that utils.lua is in:
cd "D:\Users\Mike\Dropbox\Lua Modeling"
lua main.lua
The long answer
To understand what is going wrong here, it is helpful to know a little bit about how require works. The first thing that require does is to search for the module in the module path. From Programming in Lua chapter 8.1:
The path used by require is a little different from typical paths. Most programs use paths as a list of directories wherein to search for a given file. However, ANSI C (the abstract platform where Lua runs) does not have the concept of directories. Therefore, the path used by require is a list of patterns, each of them specifying an alternative way to transform a virtual file name (the argument to require) into a real file name. More specifically, each component in the path is a file name containing optional interrogation marks. For each component, require replaces each ? by the virtual file name and checks whether there is a file with that name; if not, it goes to the next component. The components in a path are separated by semicolons (a character seldom used for file names in most operating systems). For instance, if the path is
?;?.lua;c:\windows\?;/usr/local/lua/?/?.lua
then the call require"lili" will try to open the following files:
lili
lili.lua
c:\windows\lili
/usr/local/lua/lili/lili.lua
Judging from your error message, your Lua path seems to be the following:
.\?.lua;D:\Program Files (x86)\Lua\5.1\lua\?.lua;D:\Program Files (x86)\Lua\5.1\lua\?\init.lua;D:\Program Files (x86)\Lua\5.1\?.lua
To make that easier to read, here are each the patterns separated by line breaks:
.\?.lua
D:\Program Files (x86)\Lua\5.1\lua\?.lua
D:\Program Files (x86)\Lua\5.1\lua\?\init.lua
D:\Program Files (x86)\Lua\5.1\?.lua
From this list you can see that when calling require
Lua fills in the .lua extension for you
Lua fills in the rest of the file path for you
In other words, you should just specify the module name, like this:
require("utils")
Now, Lua also needs to know where the utils.lua file is. The easiest way is to run your program from the D:\Users\Mike\Dropbox\Lua Modeling folder. This means that when you run require("utils"), Lua will expand the first pattern .\?.lua into .\utils.lua, and when it checks that path it will find the utils.lua file in the current directory.
In other words, running your program like this should work:
cd "D:\Users\Mike\Dropbox\Lua Modeling"
lua main.lua
An alternative
If you can't (or don't want to) change your working directory to run the program, you can use the LUA_PATH environment variable to add new patterns to the path that require uses to search for modules.
set LUA_PATH=D:\Users\Mike\Dropbox\Lua Modeling\?.lua;%LUA_PATH%;
lua "D:\Users\Mike\Dropbox\Lua Modeling\main.lua"
There is a slight trick to this. If the LUA_PATH environment variable already exists, then this will add your project's folder to the start of it. If LUA_PATH doesn't exist, this will add ;; to the end, which Lua fills in with the default path.
I'm new in Bioinformatics and Biopython, so I have some difficulties with it.
I was reading the Biopython (SeqIO) documentation, but when I try to execute some SeqIO.parse() commands I get FileNotFoundError.
For example, I want to get "example.fasta" file (which I don't have it on my PC). I try to do it with this command:
for record in SeqIO.parse("example.fasta", "fasta"):
print(record.id)
But, all I get is FileNotFoundError: [Errno 2] No such file or directory
Can someone help me with this?
My understanding is that FileNotFoundError occurs when the code tries to open a file on your computer and does not find it.
This can happen either because you simply do not have this file, or you gave the name with a typo, or the path to the file is not correct (This is an important notion: the path to the file should be absolute, or relative to the current working directory (usually the one from which you executed the python script)).
As suggested in the comments to your question, you seem to be expecting SeqIO.parse to get the file for you. This is not the case. The first argument you give to this function (in the example "example.fasta") is the path to an existing file that you want to "parse", that is, interpret its information content and make this content available to the rest of your program in a convenient form.
So in order to get this example working, you first need to get a fasta file. If you do not already have one, you can download some manually from genbank, or find one in the biopython installation (if you installed it from source and know where the source code is located), for instance in Tests/Quality/example.fasta.
I am recovering Stata following a Windows upgrade. I have a list of my packages generated from ado dir in the following format:
[1] package mdesc from http://fmwww.bc.edu/RePEc/bocode/m
'MDESC': module to tabulate prevalence of missing values
[2] package univar from http://fmwww.bc.edu/RePEc/bocode/u
'UNIVAR': module to generate univariate summary with box-and-whiskers plot
[3] package tabmiss from http://www.ats.ucla.edu/stat/stata/ado/analysis
tabmiss. Shows tabulation of number of missing and non-missing values
I have many packages and would like to reinstall them without having to designate each directory/url via net cd. While using net cd along with net install or ssc install along with package names in a loop is trivial (as below), it would seem that an automated method for this task might be available.
net cd http://www.ats.ucla.edu/stat/stata/ado/analysis
local ucla tabmiss csgof powerlog ldfbeta
foreach x of local ucla {
net install `x'
}
To my knowledge, there is no built-in or automated method of tracking and managing your installed packages outside of what is available through ado or net.
I would also tend to agree with #Nick Cox that this task seems strange and I can't imagine how a new Stata install or reinstall could know what was installed previously, but I find the question interesting for other reasons.
The main reason being for users who have Stata installed on multiple machines who need the same packages on both machines. I faced a similar issue when I purchased a new computer and installed Stata but wanted all of the packages I use to be available as well. Outside of moving the ado directory or selected contents I'm not aware of any quick solution.
Here it would be possible to use the output of ado dir on one machine to determine what you need to install on a second machine with a new Stata install.
The method you propose using a foreach loop could save you time from having to type in or copy/paste a lot of packages and URLs. At the same time however, this is only beneficial if you have many packages from only a few repositories because you will need to net cd to the URL each time as you show in your example.
An alternative solution is the programmatic solution. As you know, ado dir will list each installed package, the URL and a short description of the package. Using this, a log file, and the built in I/O functionality, a short program could be written to automate the process and dynamically build a do file that contains the commands to install the already installed packages.
The code below generates a do file containing commands (in this case, net describe package, from(url)) for each package I have installed on my computer.
clear *
tempfile log1
log using "`log1'", text name(mylog)
ado dir
log close mylog
tempname logfile
file open `logfile' using "`log1'", read
file read `logfile' line
file open dfh using "path/to/your/dofile.do", write replace
local pckage "package"
while r(eof) == 0 {
if `: list pckage in line' {
local packageName : word 3 of `line'
local dirName : word 5 of `line'
di "`packageName' `dirName'"
file write dfh "net describe `packageName', from(`dirName')"
file write dfh _newline
}
file read `logfile' line
}
file close `logfile'
file close dfh
In the above code, I create a temp file to write a .txt log file to and store the contents of ado dir in that file.
Then, I open the log file using file open and read it line by line in the while loop.
Above the loop, I'm creating a do file at /path/to/your/dofile.do to hold the output of the loop - the dynamically created commands relating to the installed packages on my machine.
The loop will iterate so long as r(eof) = 0, where r(eof) is an end of file marker. I use an if statement to sort out lines of the log file which contain the word package, as I'm only interested in those lines with the package name and URL in them.
Inside of the if block, I parse the local macro line to pull the package name and the URL/directory name.
this is important: this section of code assumes that the 3rd and 5th words in the macro will always be the package name and URL respectively - Confirm this from the output of ado dir before executing.
You will also need to change the command that is being written to the file handle dfh inside of the loop to what you want (net install, etc) when you are ready to execute.
For more help on using file, locals, and tempfiles execute any of the following in Stata:
help file
help extended_fcn
help macrolists
There may be nicer ways to parse the contents of ado dir but this has worked for me. And of course I'd always advise that you take the time to understand what the code is doing so that you can make any necessary tweaks to fit your particular situation.
I'm using Lua in interactive mode on a Mac (thanks to rudix.org).
When I want to load a file I do:
dofile("/my/long/path/to/my/directory/file.lua")
I want to do a different thing, that is:
put all my files in a desktop directory myDirectory;
then call the file from the terminal this way dofile("file.lua");
Is this possible? How?
If the path is fixed, you can just redefine dofile:
local _dofile=dofile
local path=("/my/long/path/to/my/directory/")
function dofile(x)
return _dofile(path..x)
end
You may put this (and other initializations) in a file and set the environment variable LUA_INIT to its location. After this, every invocation of lua will see the version of dofile redefined above and the users will be able to say simply dofile("foo.lua").
Alternatively, you can use require, which looks for modules in a list of paths in package.path or LUA_PATH.
I need to run some shell commands on a number of files and sometimes I get back more than one file in response. The question is: How can I read back several files from IO.popen in Ruby?
For instance, imagine the following case:
file = grid.get(record['_id']) # fetch a file from database
IO.popen('tar -Oxmz', 'ab') {|pipe| pipe.write(file.read)} # pass to tar and extract
This necessitates that I reread all the extracted files from the filesystem. I figured out this is the speed bottleneck of my script and I wonder if I can accomplish the same task in-memroy. I tried the following:
file = grid.get(record['_id'])
IO.popen('tar -Oxmz', 'w+b') do |pipe|
pipe.write(file.read)
pipe.close_write
output = pipe.read
end
It works, but I get the whole response, here including several extracted files, in one piece (in variable output). I need the files separate from each other and possibly with their names. Is there any way to do this?
By the way, the resulting files are most of the time text, but sometimes binary. Running a pipe for each output file is not a solution, because the actual overhead of running the commands for each file outweights the benefits of doing the transformation in-memory.
P.S. The actual use case does not rely on tar only. I use software that do not have Ruby wrappers.