for i = 1, 20 do --Create a loop
if i < 10 then
local function LessThan10()
return i
end
end
end
print(LessThan10())
Surprisingly, eventhough LessThan10 was inside a conditional statement and it was a local function(actually it's not the function, it's the variable). Somehow, I could still print out the answer
This is pretty interesting (I checked in Zerobrane, LessThan10 is a local function)
EDIT : Well I guess it's my interpreter problem, I changed the interpreter and this thing errors.
Tested in Lua 5.0 interpreter:
Lua 5.0.3 Copyright (C) 1994-2006 Tecgraf, PUC-Rio
> for i = 1, 20 do --Create a loop
>> if i < 10 then
>> local function LessThan10()
>> return i
>> end
>> end
>> end
> print(LessThan10())
stdin:1: attempt to call global `LessThan10' (a nil value)
stack traceback:
stdin:1: in main chunk
[C]: ?
I also can't believe this is / was valid code as local variables are only visible within the block they are declared at.
If you are using a custom Lua interpreter you should further investigate on it, seems pretty interesting though.
I tested this and it only worked on Lua 5.0 and 5.1
I tested it again on Lua 5.3 and it no longer works
My zerobrane reset my lua version to 5.0 for no reason, well, sorry if this question disappointed you.
When I run any pystan code, the output is what I expect, but I get a wall of warnings.
I've tried updating pystan and cython, as these are mentioned in the wall of warnings. My pystan is now version 2.17.1 and cython 0.29.2. I'm running python3.7.
import pystan
model_code = 'parameters {real y;} model {y ~ normal(0,1);}'
model = pystan.StanModel(model_code=model_code) # this will take a minute
y = model.sampling(n_jobs=1).extract()['y']
y.mean() # should be close to 0
The error message that I get starts with:
/home/femke/anaconda3/lib/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/tmp8_plkepg/stanfit4anon_model_5944b02c79788fa0db5b3a93728ca2bf_5335140894361802645.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /home/femke/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1823:0,
from /home/femke/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/femke/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /tmp/tmp8_plkepg/stanfit4anon_model_5944b02c79788fa0db5b3a93728ca2bf_5335140894361802645.cpp:688:
/home/femke/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^~~~~~~
In file included from /home/femke/anaconda3/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.66.0/boost/numeric/ublas/matrix.hpp:19:0,
from /home/femke/anaconda3/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.66.0/boost/numeric/odeint/util/ublas_wrapper.hpp:24,
from /home/femke/anaconda3/lib/python3.7/site-packages
Is this something to worry about? If not, how do I specifically disable these warnings, but not from other parts of my code? If so, what should I change.
Edit: after having read the question Cython Numpy warning about NPY_NO_DEPRECATED_API when using MemoryView, I still don't know how to safely disable this warning.
I'm running blastx on my de novo transcriptome assembly. While the program is still running I've been obtaining errors like this one:
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 1127 characters (max is 1000)
...and others, where the number of characters varies. I've searched for this specific error online but I don't seem to find anything regarding it. I was hoping that someone that has run across it can help me understand what it means and specially, if I should stop the run and start with different parameters or make some change to my assembly.
I'm facing the same problem in the ncbi-blast-2.2.29+ version.
Then, I used an older version (2.2.25+) and makeblastdb worked fine to me, without these two message errors:
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 1141 characters (max is 1000)
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.
Well, you can use an older version too, until the developers fix the problem.
Did you ever figure this out? I'm running into the same issue with fasta files generated by a Trinity assembly. The fasta file is not altered in any way, so I'm not sure why there would be a problem. I did some research and found the source code that generates this error:
void CFastaReader::ParseTitle(
00848 const SLineTextAndLoc & lineInfo, IMessageListener * pMessageListener)
00849 {
00850 const static size_t kWarnTitleLength = 1000;
00851 if( lineInfo.m_sLineText.length() > kWarnTitleLength ) {
00852 FASTA_WARNING(lineInfo.m_iLineNum,
00853 "FASTA-Reader: Title is very long: " << lineInfo.m_sLineText.length()
00854 << " characters (max is " << kWarnTitleLength << ")",
00855 ILineError::eProblem_TooLong, "defline");
00856 }
This code was found at: enter link description here
I ended up using a one-liner to parse the extraneous information out of the fasta headers:
sed -e 's/>* .*$//' original.fasta > truncated.fasta
But I'd recommend doing that on a test file first, as your headers are most likely going to be different than mine.
Thanks for the pointer!
I get this error message:
"Strict Standards: Creating default object from empty value in /opt/lampp/htdocs/projects/nusoap/lib/nusoap.php on line 76 "
The code on line 76:
$GLOBALS['_transient']['static']['nusoap_base']->globalDebugLevel = 9;
What does this mean? And how can I fix it.
Looking forward to your reply
Regards
SirBT
You can set the error_reporting level to strict just before include nusoap library:
ini_set('error_reporting', E_STRICT);
require 'nusoap.php';
I fixed the problem by replacing the nusoap.php file with a an older version specifically nusoap.php 0.95.
The PHP environment I work in is: PHP 5.3.8, nusoap.php 0.95 seems to be compatible with PHP 5.3.8. My conclusion is that the: "Strict Standards: Creating default object from empty value in /opt/lampp/htdocs/projects/nusoap/lib/nusoap.php on line 76" is a compatibility issue.
The Octave documentation on this subject is both intimidating and sparse.
I did not know where else to document the solution I found, so I am posting here. I apologize if that's inappropriate, but I want to help the next guy.
The following solution is for a simple windows distributable.
Use Case:
A solution is developed in Octave 3.2.4, and needs to be distributed to end-users with few computer skills. Installing and explaining Octave is impossible, the solution must be "one-click" or "brain-dead-simple."
Known Issues:
imread fails in 3.2.4 because file_in_path.m is wrong. You will need to update the file file_in_path.m to the following (just replace it):
function name=file_in_path(p,file)
idx=[1 findstr(p,pathsep) length(p)+1];
for i=1:length(idx)-1
if idx(i+1)-idx(i)<=1
dir=strcat(pwd,"/");
else
dir=p(idx(i)+1:idx(i+1)-1);
end
name = fullfile(dir, file);
fid = fopen(name,"r");
if fid >= 0
fclose(fid);
return
end
end
fid = fopen(file,"r");
if fid >= 0,
fclose(fid);
name=file;
return
end
name=[];
Solution: Create a distributable exe using mkoctfile, and package this exe with the core Octave files, and other .oct and .m files as necessary.
Step 1: Create a stand-alone executable.
You can see code that works here:
http://www.gnu.org/software/octave/doc/interpreter/Standalone-Programs.html
Particularly the file "embedded.cc".
I have simplified that file as follows:
#include <iostream>
#include <octave/oct.h>
#include <octave/octave.h>
#include <octave/parse.h>
int
main (int argc, char *argvc[])
{
string_vector argv (2);
argv(0) = "embedded";
argv(1) = "-q";
octave_main (2, argv.c_str_vec(), 1);
octave_value_list in = octave_value (argvc[1]);
octave_value_list out = feval ("your_custom_m_file", in);
if (!error_state && out.length () > 0)
{
}
else
{
std::cout << "invalid\n";
}
return 0;
}
Build this file with the command
mkoctfile --link-stand-alone embedded.cc -o embedded
It may throw warnings, but as long as it throws no errors, you should be fine. The file embedded.exe will be built, and can be run. The only issue is that it will lack all the goodies that make octave awesome. You will have to provide those.
Step 2: Create a distribution folder
You will need to create a copy of many of the Octave files. I suggest a directory specifically for this. At a minimum, you will need a copy of all or most of the DLLs in \bin. Additionally, place your distributable executable in this directory.
Step 3: Other files whack-a-mole
You will now need to find out what other files will be necessary to run your .m script. You can simplify this step by copying \oct\i686-pc-mingw32*.oct and \share\octave\3.2.4\m\*\*.m to the distribution directory, although this will be overkill, and will not actually prevent the whack-a-mole step.
Now, you must play whack-a-mole or the time-honored tradition of "where my includes be at, yo?"
Open a cmd prompt and navigate to your distribution folder.
Get rid of any useful PATH strings. Your customers won't have them.
Attempt to run the program embedded.exe. You will get an error such as the following:
embedded.exe
error: `max' undefined near line 83 column 22
error: evaluating argument list element number 1
error: evaluating argument list element number 1
error: called from:
error: T:\sms\Development\research\c2\disttest\strcat.m at line 83, column 3
error: T:\sms\Development\research\c2\disttest\file_in_path.m at line 5, column 10
error: T:\sms\Development\research\c2\disttest\imread.m at line 50, column 6
A Search in your Octave installation for "max". It will either be a .oct or a .m file. In this case, it is a .oct file, max.oct. Copy it to your distribution directory.
B You search for something obvious like "min", and get no results. This is because the Loadable Function "min" is in the .oct file "max.oct". Make a copy of max.oct, and rename it to min.oct. It will work now. How do you know where the functions are? I'm not sure. Most of them are in obvious places like "max.oct" for min, and "fft2.oct" for "ifft2.oct". Good luck with all that.
Repeat until your executable runs.
Just to add that if you want to run a script instead of an m function, then the line of the embedded.cc:
octave_value_list out = feval ("your_custom_m_file", in);
should be:
octave_value_list out = feval ("your_custom_m_script");
Also use 'which' to find where the missing functions are packed. For example for the min function:
octave:22> which min
min is a function from the file C:\Octave\Octave3.6.2_gcc4.6.2\lib\octave\3.6.2\oct\i686-pc-mingw32\max.oct
Something I found when linking my custom m file into an Octave standalone:
Needed #include <octave/toplev.h>
Replace return 0; (as above) with clean_up_and_exit(0);
Without these steps my program repeatedly crashed on exit.
Run mkoctfile --link-stand-alone embedded.cc -o embedded
from the octave solution and not from a batch file.
Just saved you half day (-;
In the above solution in bullet 4 B:
B You search for something obvious like "min", and get no results.
This is because the Loadable Function "min" is in the .oct file
"max.oct". Make a copy of max.oct, and rename it to min.oct. It will
work now.
This might not work if some function is being called from #folder function.m and also to avoid unnecessary duplicated files, just add the following code somewhere in your m file outside #folder
autoload ("min", "max.oct");
Likewise, it can be removed via
autoload ("min", "max.oct", "remove");
Ensure that the path to max.oct is provided here.
The above understanding is based on a file PKG_ADD and PKG_DEL in the communications package located at \Octave-4.0.1\lib\octave\packages\communications-1.2.1\i686-w64-mingw32-api-v50+\
Check out Stratego Octave Compiler.
(I've not tested it yet, but plan to do so in the next few days.)
I had that very same requirement (one-click, brain-dead-simple), so I made a setup that contained only curl.exe, the batch file below, an exe which was a .bat in disguise (simply calling the batch file below) and the .vbs script below (not writen by me). And of course my m-file.
This will download Octave 4.2.1 as a portable program (32 bit, otherwise we'dd have to download again if the system turns out to be 32 bit), unpack using the vbs script, move the contents to the same folder as the batch file and run it in GUI mode. Every next time the same script is called, it will only check if octave.bat is still there.
Of course this results in a huge waste of disk space, downloading the 280MB zip, which unpacks to over 1GB (which I make even worse by not deleting the zip afterwards), and you're stuck with a cmd window that is not easy to hide.
But it does offer the simplest solution I could find. It is also less likely to break in the future (either with an update of your own, or an update from Octave). Some glorious day, mkoktfile will actually be easy to use and will solve dependencies on its own, but until that day this remains the least headache-inducing solution I could find. And aspirins are more expensive than someone else's disk space.
::this file will test if the octave portable is downloaded and unpacked
#ECHO OFF
SET my_m_file=your_mfile.m
SET name_of_this_script=run_me.bat
::if the file exists, skip to the actual running.
IF EXIST "octave.bat" goto OctaveIsExtracted
IF EXIST "octave-4.2.1-w32.zip" goto OctaveIsDownloaded
ECHO The runtime (Octave portable 4.2.1) will now be downloaded.
ECHO This may take a long time, as it is about 280MB.
ECHO .
ECHO If this download restarts multiple times, you can manually download the octave-4.2.1-w32.zip from the GNU website. Make sure to unpack the contents.
::if this errors, you can uncomment the line with archive.org (which doesn't report total size during download)
curl http://ftp.gnu.org/gnu/octave/windows/octave-4.2.1-w32.zip > octave-4.2.1-w32.zip
::curl http://web.archive.org/web/20170827205614/https://ftp.gnu.org/gnu/octave/windows/octave-4.2.1-w32.zip > octave-4.2.1-w32.zip
:OctaveIsDownloaded
::check to see if the file size is the correct size to assume a successful download
::if the file size is incorrect, delete the file, restart this script to attempt a new download
::file size should be 293570269 bytes
call :filesize octave-4.2.1-w32.zip
IF /I "%size%" GEQ "293560000" goto OctaveIsDownloadedSuccessfully
del octave-4.2.1-w32.zip
::start new instance and exit and release this one
start %name_of_this_script%
exit
:OctaveIsDownloadedSuccessfully
IF EXIST "octave.bat" goto OctaveIsExtracted
::unzip and move those contents to the current folder
ECHO Unzipping octave portable, this may take a moment.
cscript //B j_unzip.vbs octave-4.2.1-w32.zip
SET src_folder=octave-4.2.1
SET tar_folder=%cd%
for /f %%a IN ('dir "%src_folder%" /b') do move %src_folder%\%%a %tar_folder%
pause
:OctaveIsExtracted
octave.bat %my_m_file%
goto :eof
:filesize
set size=%~z1
exit /b 0
And j_unzip.vbs
' j_unzip.vbs
'
' UnZip a file script
'
' By Justin Godden 2010
'
' It's a mess, I know!!!
'
' Dim ArgObj, var1, var2
Set ArgObj = WScript.Arguments
If (Wscript.Arguments.Count > 0) Then
var1 = ArgObj(0)
Else
var1 = ""
End if
If var1 = "" then
strFileZIP = "example.zip"
Else
strFileZIP = var1
End if
'The location of the zip file.
REM Set WshShell = CreateObject("Wscript.Shell")
REM CurDir = WshShell.ExpandEnvironmentStrings("%%cd%%")
Dim sCurPath
sCurPath = CreateObject("Scripting.FileSystemObject").GetAbsolutePathName(".")
strZipFile = sCurPath & "\" & strFileZIP
'The folder the contents should be extracted to.
outFolder = sCurPath
'original line: outFolder = sCurPath & "\"
WScript.Echo ( "Extracting file " & strFileZIP)
Set objShell = CreateObject( "Shell.Application" )
Set objSource = objShell.NameSpace(strZipFile).Items()
Set objTarget = objShell.NameSpace(outFolder)
intOptions = 256
objTarget.CopyHere objSource, intOptions
WScript.Echo ( "Extracted." )