Broken pipe issue - octave

I'm trying to learn machine learning using Octave.
OS: Mac, High Sierra 10.13.3
GNU Octave version: 3.8.0
t = [0: 0.01: 0.98];
y1 = sin(2*pi*4*t);
y2 = sin(2*pi*4*t);
plot(t, y1);
hold on;
plot(t, y2, 'r');
figure(1); plot(t,y1);
The first time I tried ran the last line I got: "Qt terminal communication error: select() error 9 Bad file descriptor"
After this I got a broken pipe error, I thought I need to plot both the graphs again before trying "figure(1); plot(y,t1);". But, it didn't work.
Checked whois and printed the values of y1, y2 and t; they do exist. So, my questions are:
Why am I not able to plot the graphs?
How do I solve broken pipe error?
How to solve the Qt terminal communication error?

Coursera's Machine Learning class is still using this version of Octave (3.8.0)
Here is what helped me:
run the following the os x terminal:
brew uninstall gnuplot
brew install gnuplot --with-qt
then create a file in your home directory called .octaverc and add the following to it:
setenv("GNUTERM","qt")
Relaunch octave-cli
Good Luck!

simply close the terminal and relaunch it , and this fixes the issue.
This occurred to me as I tried quitting the gnu-plot instead of using close command causing the pipe linked to gnu be broken.

Related

unable to install any pkg in Octave

I am new to Octave, coming from Matlab. I am trying to install a few packages, and so far none has worked. I have tried the download method from forge, then running the install command. But my question is about my latest attempt. There it is:
pkg install -global -forge io
csvconcat.cc:79:37: warning: result of comparison of constant 18446744073709551615 with expression of type
'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
while ((pos=str.find(prot, pos)) != str.npos) {
~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~
1 warning generated.
error: couldn't append to /Applications/Octave-4.4.1.app/Contents/Resources/usr/Cellar/octave-octave-app#4.4.1/4.4.1/share/octave/octave_packages
save: unable to open output file '/Applications/Octave-4.4.1.app/Contents/Resources/usr/Cellar/octave-octave-app#4.4.1/4.4.1/share/octave/octave_packages'
error: called from
install at line 254 column 7
pkg at line 437 column 9
Couldn't find any documentation on it, I am a bit lost.... (oh and btw, I can't find the config.log file! where is that gem?)
I am on MacOS catalina 10.15.7, and just followed that procedure https://flaviocopes.com/fix-xcrun-error-invalid-active-developer-path/, which solved the issues I had before which is described on that page.
cheers for any help
The error:
error: couldn't append to /Applications/Octave-4.4.1.app/Contents/Resources/usr/Cellar/octave-octave-app#4.4.1/4.4.1/share/octave/octave_packages
save: unable to open output file '/Applications/Octave-4.4.1.app/Contents/Resources/usr/Cellar/octave-octave-app#4.4.1/4.4.1/share/octave/octave_packages'
error: called from
install at line 254 column 7
pkg at line 437 column 9
basically says it's failing to save to that file. Probably a permissions issue. Check if the file /Applications/Octave-4.4.1.app/Contents/Resources/usr/Cellar/octave-octave-app#4.4.1/4.4.1/share/octave/octave_packages exists and its permissions. That file is a database of all packages installed globally, i.e., for all users in the system.
Fixing the permission issues is dependent on what is the permissions issue you have (probably you need to run octave as root to install a global package). But maybe try to install the package for your user only, i.e., install the package without the -global flag, like so:
pkg install -forge io

Octave Symbolic Error- "Error in var export"

I am having a tough time with the symbolic package in octave.
Software Versions (downloaded everything today):
-Octave: 4.0.0
-OctSymPy 2.2.2
-Python: 3.4
-SymPy: 0.7.6
When I try to multiply/divide/raise to a power symbolic variables, I get the following error:
PYTHON: Error in var export
Resetting the octsympy communication mechanism
Closing the Python pipe...
error: python_cmd: unexpected return
error: called from
python_cmd at line 143 column 6
mtimes at line 42 column 5
syms X Y
X*Y
I am totally stumped. Does anyone have any ideas on the cause of this? I can add and differientiate symbolic expressions, so it is working to some extent.
Thanks!
I had the same problem and I just have downloaded and installed the python version 2.7.11 and worked fine.
Ah, don't forget to reinstall SimPy, but this time on the new Python version.
When you get back to octave, it'll recognize that version.

error installing octcdf-1.1.5

I Have in my Mac:
Octave-3.4.0
Gnuplot 4.2 - that I had to install because I had problems plotting - it wouldn't plot at all.
I need to load a netcdf file, the error that came was:
nc = netcdf('/users/matheuscortezi/Desktop/Pcse005/ocean_avg.nc', 'r')
error: `netcdf' undefined near line 9 column 6
So I think I don't have the netcdf comand installed, and tried installing by typing this on octave:
pkg install -global -forge octcdf
The error message that I receive from that is:
configure: error: in `/var/tmp/oct-t8XcYD/octcdf/src':
configure: error: C compiler cannot create executables
See `config.log' for more details.
the configure script returned the following error: checking for gcc... /usr/bin/gcc-4.2
checking whether the C compiler works... no
error: called from `pkg>configure_make' in file /Applications/Octave.app/Contents/Resources/share/octave/3.4.0/m/pkg/pkg.m near line 1325, column 9
error: called from:
error: /Applications/Octave.app/Contents/Resources/share/octave/3.4.0/m/pkg/pkg.m at line 783, column 5
error: /Applications/Octave.app/Contents/Resources/share/octave/3.4.0/m/pkg/pkg.m at line 354, column 9
I haven't the faintest idea about what I should do. How can I solve this problem with either:
fixing this error, or
installing a netcdf "comand pack" (i don't know the name for that) so I can use netcdf() as in the example given.
Hope I was clear enough.
It seems to me that you installed Octave from the Mac OSX App bundle. That is not recommended at all. You should install from one of the package managers as explained on Octave's wiki. As far as I know, there are 3 options for Mac (see previous link). Just search for one that also has the netcdf package.
Anyway, if you really don't want to install it through a package manager (but seems to me you really should), seems that your problem lies on gcc (the GNU C compiler). do you have it installed at all? Some packages have code in C++ or C and are also dependent on some external libraries.
EDIT using a package manager would have also solved your problem about plotting since it would install gnuplot at same time

Installation error for DBD::MySQL on OSX v10.6.6

I'm attempting to get DBD::MySQL working on Snow Leopard (v10.6.6). The default version of Perl that comes with the OS is v5.10.0. Since I've read that's 64-bit, I went ahead and downloaded and installed a 64-bit version of MySQL (mysql-5.5.8-osx10.6-x86_64).
Installing and setting up MySQL went smoothly, here's my config and version number for reference.
I used CPAN to download DBI and the DBD::MySQL drivers. I then:
Installed DBI
Setup a Makefile.PL
Ran the make command from the command line
The Makefile.PL said it would use the following settings for compiling and testing:
I will use the following settings for compiling and testing:
cflags (mysql_config ) = -I/usr/local/mysql/include -Os -g -fno-common -fno-strict-aliasing -arch x86_64
embedded (mysql_config ) =
libs (mysql_config ) = -L/usr/local/mysql/lib -lmysqlclient -lpthread
mysql_config (guessed ) = mysql_config
nocatchstderr (default ) = 0
nofoundrows (default ) = 0
ssl (guessed ) = 0
testdb (default ) = test
testhost (default ) =
testpassword (User's choice) = r00t!
testsocket (default ) =
testuser (User's choice) = root
To change these settings, see 'perl Makefile.PL --help' and
'perldoc INSTALL'.
Multiple copies of Driver.xst found in: /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBI/ /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level/auto/DBI/ at Makefile.PL line 907
Using DBI 1.616 (for perl 5.010000 on darwin-thread-multi-2level) installed in /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBI/
Writing Makefile for DBD::mysql
Everything seemed to be going fine, until I tried to run make test :
t/00base....................NOK 2/6# Tried to use 'DBD::mysql'.
# Error: Can't load '/Users/swm/.cpan/build/DBD-mysql-4.018-Pnd2qz/blib/arch/auto/DBD/mysql/mysql.bundle' for module DBD::mysql: dlopen(/Users/swm/.cpan/build/DBD-mysql-4.018-Pnd2qz/blib/arch/auto/DBD/mysql/mysql.bundle, 2): Library not loaded: libmysqlclient.16.dylib
# Referenced from: /Users/swm/.cpan/build/DBD-mysql-4.018-Pnd2qz/blib/arch/auto/DBD/mysql/mysql.bundle
# Reason: image not found at /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line 207.
# at (eval 7) line 2
# Compilation failed in require at (eval 7) line 2.
# BEGIN failed--compilation aborted at (eval 7) line 2.
FAILED--Further testing stopped: Unable to load DBD::mysql
make: *** [test_dynamic] Error 9
It's failing because it can't seem to find the mysql.bundle for DBD. Has anyone come across this problem? Or can point me in the right direction on what to try next? I need DBI/DBD::MySQL for my new job and I'm scrambling to find a solution.
Many thanks in advance.
I got around the "Library not loaded: libmysqlclient.16.dylib" problem by placing a symbolic link in /usr/lib/" to /usr/local/mysql-5.5.8-osx10.6-x86_64/lib/libmysqlclient.16.dylib
I worked around the same or a similar issue. Somehow I could build and test DBD::mysql with cpan but when I tried to use it in a script it said things like
dyld: lazy symbol binding failed: Symbol not found: _mysql_init
Referenced from: /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle
Expected in: flat namespace
Apparently, it's a 64-bit vs 32-bit issue.
Installing the fink dbd-mysql-pm5100 package made it work though it took kind of a long time. I also removed the cpan-installed version:
sudo rm -rf /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBD/mysql
sudo rm -rf /Library/Perl/5.10.0/darwin-thread-multi-2level/DBD/mysql
sudo rm -rf /Library/Perl/5.10.0/darwin-thread-multi-2level/DBD/mysql.pm
also include in .profile
export VERSIONER_PERL_PREFER_32_BIT=yes;
Besides creating the link the executions of the program with DBI::mysql generated an error, thus including this variable on the environment make it works
I know this is an old post. But I suppose the best solution would be to add the library directory to the DYLD_FALLBACK_LIBRARY_PATH env variable. (reason here: https://stackoverflow.com/a/3172515/119958 )
There is no ldconfig in mac, so just add the path to this env var and rerun the install process for DBD::mysql
Donato-Vianas-MacBook-Pro:Invoicer donato$ cpanm DBD::mysql
--> Working on DBD::mysql
Fetching http://www.cpan.org/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.022.tar.gz ... OK
Configuring DBD-mysql-4.022 ... OK
Building and testing DBD-mysql-4.022 ... FAIL
! Installing DBD::mysql failed. See /Users/donato/.cpanm/build.log for details.
# Failed test 'use DBD::mysql;'
# at t/00base.t line 21.
# Tried to use 'DBD::mysql'.
# Error: Can't load '/Users/donato/.cpanm/work/1359948144.491/DBD-mysql-4.022/blib/arch/auto/DBD/mysql/mysql.bundle' for module DBD::mysql: dlopen(/Users/donato/.cpanm/work/1359948144.491/DBD-mysql-4.022/blib/arch/auto/DBD/mysql/mysql.bundle, 2): Library not loaded: libmysqlclient.18.dylib
Donato-Vianas-MacBook-Pro:Invoicer donato$ export DYLD_FALLBACK_LIBRARY_PATH=/usr/local/mysql/lib/:$DYLD_FALLBACK_LIBRARY_PATH
Donato-Vianas-MacBook-Pro:Invoicer donato$ cpanm DBD::mysql--> Working on DBD::mysql
Fetching http://www.cpan.org/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.022.tar.gz ... OK
Configuring DBD-mysql-4.022 ... OK
Building and testing DBD-mysql-4.022 ... OK
Successfully installed DBD-mysql-4.022
1 distribution installed
Donato's solution works for install, but the var has to be present at runtime as well or I get the same error. The following fixes this at runtime for shell and _www user:
# For command line use, add following line to ~/.bash_profile:
export DYLD_FALLBACK_LIBRARY_PATH=/usr/local/mysql/lib/:$DYLD_FALLBACK_LIBRARY_PATH
# If Apache needs it, add following line to /etc/apache2/httpd.conf:
# On Lion Server, I put it after <IfDefine MACOSXSERVER>, but shouldn't matter
SetEnv DYLD_FALLBACK_LIBRARY_PATH /usr/local/mysql/lib/:$DYLD_FALLBACK_LIBRARY_PATH
It's somewhat of an aside, but I strongly recommend setting up a separate perl on the machine -- either by fink / macports, or from source -- and leaving the Mac's system perl (and its libraries) alone.
Once I did this on my own Mac, I had very few troubles installing modules thereafter, and I didn't have to worry about accidentally blowing a hole in my OS by breaking the perl that the system uses.
If it were my Mac, I'd install a new perl from source (the Perl source distribution is smart enough to install itself see that it's on a Mac and install itself safely into /usr/local/bin) and the proceed from thee to install DBD::Mysql (and the other modules you require).

Win7 MInGW QT MySQL program screams "cannot find -lqsqlmysqld"; where is the missing library?

I am attempting to make a qt program on Windows 7 that uses a MySQL plugin.
I have compiled both qt and the mysql plugin with no problems using my minGW 32bit compiler.
However, I keep on getting an error like this:
mingw32-make -f Makefile.Debug
mingw32-make[1]: Entering directory `C:/Users/dhatt/Desktop/testdb2'
g++ -c -g -frtti -fexceptions -mthreads -Wall -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_DLL -DQT_SQL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_THREAD_SUPPORT -DQT_NEEDS_QMAIN - I"..\..\..\..\QT\qt\include\QtCore" -I"..\..\..\..\QT\qt\include\QtGui" -I"..\..\..\..\QT\qt\include\QtSql" -I"..\..\..\..\QT\qt\include" -I"..\..\..\..\MySQL\bin" -I"..\..\..\..\QT\qt\include\ActiveQt" -I"debug" -I"..\..\..\..\QT\qt\mkspecs\win32-g++" -o debug\database.o database.cpp
g++ -enable-stdcall-fixup -Wl,-enable-auto-import -Wl,-enable-runtime-pseudo-reloc -mthreads -Wl -Wl,-subsystem,windows -o debug\testdb2.exe debug/database.o -L"c:\QT\qt\lib" -lmingw32 -lqtmaind -L C:\MySQL\lib\opt -LC:/QT/qt/plugins/sqldrivers -lqsqlmysqld -lQtSqld4 -lQtGuid4 -lQtCored4 -LC:\MySQL\lib\opt
C:/qt/mingw/bin/../lib/gcc/mingw32/4.4.0/../../../../mingw32/bin/ld.exe: cannot find -lqsqlmysqld
collect2: ld returned 1 exit status
mingw32-make[1]: *** [debug\executable.exe] Error 1
mingw32-make[1]: Leaving directory `C:/Users/dhatt/Desktop/testdb2'
mingw32-make: *** [debug] Error 2
I apologize in advance for being very verbose of what I did, but I am doing this partly for troubleshooting, and partly so any other lost souls don't end up wasting three weeks on this particular problem. :)
Here are my specs:
Windows 7 Nokia's Open Source QT
Qt SDK for Windows (C:\Qt\2010.04\qt)
Linux MinGW Version 5.1.6 (C\Linux\MinGW)
MySQL5 with C++ files (C:\MySQL5)
If you want to know how I installed qt, just follow this site's instructions:
http://www.jiggerjuice.net/software/qt-sql-drivers.html
These other sites may hold some extra information tidbits:
http://doc.qt.nokia.com/4.6/sql-driver.html
http://www.rag.com.au/linux/qt4howto.html
http://qtnode.net/wiki?title=Qt4_on_Windows (yes, I did check with Nokia's docs!!!)
http://doc.trolltech.com/qq/qq10-windows-deployment.html
This fellow mentioned about remaking qmake, which I am not doing unless I have a good reason.
http://christopher.rasch-olsen.no/2009/04/14/qt-45-and-mysql-plugin-with-mingw-on-windows-xp/
I've already deleted the plugin cache once before, I hope I won't have to do it again...
http://doc.trolltech.com/4.2/plugins-howto.html#the-plugin-cache
http://ubuntuforums.org/showthread.php?t=1070155
If there is any confusion, between the two compilation option (creating the mysql libraries statically, or as a plugin), I chose for the plugin because it compiles quicker and I don't have to worry about licensing.
Generally, the big trouble of mysql to most people is to make a mingw compatible library. Generally, I did this with the mingw tools in ( https://olex.openlogic.com/packages/mingw-utils )...
c:\> cd MySQL\lib\opt
c:\mysql\lib\opt> reimp -d libmysql.lib
c:\mysql\lib\opt> dlltool --input-def libmysql.def --dllname libmysql.dll --output-lib libmysql.a -k
I should have done it right since in my C:\MySQL\lib\opt, it has the two files:
libmysql.a
libmysql.lib
LIBMYSQL.def (not a typo)
and in the C:\MySQL\bin directory, I have:
libmySQL.bin (not a typo)
I had compiled the mysql plugin beforehand:
cd %QTDIR%\src\plugins\sqldrivers\mysql
qmake "INCLUDEPATH+=C:\MySQL\include" "LIBS+=C:\MYSQL\lib\opt\libmysql.lib" mysql.pro
mingw32-make
As a result, I have in my C:\QT\qt\plugins\sqldrivers folder:
libqsqlmysql4.a
libqsqlmysqldq4.a
libqsqlodbc4.a
libqsqlodbcd4.a
qsqlmysql4.dll
qsqlmysqld4.dll
qsqlodbc4.dll
qsqlodbc4.dll
And in my C:\QT\bin folder
QtSql4.dll
QtSqld4.dll
So, I assume from this site ( http://www.qtforum.org/article/21352/how-to-compile-use-a-mysql-driver.html) that I got it right.
I didn't use the binaries of qt itself, I used the compiled qt files(also from Nokia), but reconfigured and recompiled them using mingw32-make. I had no errors. This was my configuration options for remaking qt.
-opensource
-nomake examples
-nomake demos
-no-sql-lite
-no-qt3support
-no-gif
-no-libpng
-no-libmng
-no-libtiff
-no-phonon
-no-phonon-backend
-no-multimedia
-no-audio-backend
-no-webkit
-no-script
-no-scripttools
-nodeclarative
-plugin-sql-mysql -l mysql -I C:\QT\qt\include -L C:\QT\qt\lib\opt
Here is my .pro file
LANGUAGE = C++
TEMPLATE = app
TARGET = executable
QT += core sql
QTPLUGIN += qsqlmysql
DEPENDPATH += .
INCLUDEPATH += C:\MySQL\bin
LIBS += -L C:\MySQL\lib\opt -lmysql
# Input
SOURCES += database.cpp
I installed the plugin described in here:
C:\QT\qt
My path variables are:
%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\QuickTime\QTSystem\;C:\Python26;C:\Linux\Cygwin\bin;C:\mingw-utils-0.3\bin;C:\QT\qt\bin;C:\MySQL\bin;C:\MySQL\include;C:\QT\mingw32\bin;C:\QT\mingw\bin;C:\QT\qt\plugins\sqldrivers
The qt command prompt added a few extra though, so I did all of this in the command prompt.
Setting up a MinGW/Qt only environment...
-- QTDIR set to C:\QT\qt
-- PATH set to C:\QT\qt\bin
-- Adding C:\QT\bin to PATH
-- Adding C:\Windows\System32 to PATH
-- QMAKESPEC set to win32-g++ (mingw is my only compiler so, this is unnecessary)
Although I either did all that already, or it is redundant. I only add this for the sake of completeness.
Here is my code (database.cpp):
#include <QtSql>
#include <iostream>
using namespace std;
int main( int argc, char ** argv )
{
QSqlDatabase db = QSqlDatabase::addDatabase("QMYSQL");
db.setHostName("---.---.---.---");
db.setDatabaseName("--------");
db.setUserName("------------");
db.setPassword("------------");
if (!db.open()) cout << "Failed to connect to mysql" << endl;
else cout << "Works finally." << endl;
QSqlDatabase::removeDatabase("QMYSQL");
exit ( 0 );
}
Very simple, yes?
I went to my directory with the example code, run
mingw32-make distclean
qmake
mingw32-make
and get the error message above. I've tried building a version with the release version only (no debug), and it still shows the same message, but with "cannot find -lqsqlmysq", so it is not that.
I've tried many things, but where should I look next to solve it; maybe someone can narrow it down for me, set me on the right path, or even better, solve his annoying problem.
Also, I plan to use python bindings with my code (I need PyQT + MySQL). If the proposed solution would prevent me from doing so, let me know.
Well, I'm going to solve my own problem, again, so let's make this fun!
This is your last chance.
After this, there is no turning back.
You download the PyQT.exe, the story ends. You wake up in your bed and you believe whatever you want to believe. You modify the .pro file, you stay in wonderland. And, I show you how deep the rabbit hole goes.
I eventually gave up and downloaded the .exe, which does have MySQL support out of the box. If mysql does not work, your application is the problem, and I recommend you read this post here ( http://lists.trolltech.com/qt-interest/2006-06/thread00292-0.html ) or follow the quote below:
The issue is that you either have to
use the addLibraryPath method or
create a QCoreApplication instance
before your first call to loading a
database
Believe me, manually installing PyQT+MySQL on Windows is a pain. But if you need some out of the way plugin to get at that the executable doesn't know, you have to go down the rabbit hole further.
Here is the new and improved .pro file:
LANGUAGE = C++
TEMPLATE = app
TARGET = executable
QT += core sql
QTPLUGIN += qsqlmysql
DEPENDPATH += .
INCLUDEPATH += C:\MySQL\bin
LIBS += -L C:\MySQL\lib\opt
# Input
SOURCES += database.cpp
Turns out I did have the right path to mysql, I was just confusing it with the .pro file that I had. After redownloading qt and following the steps above again, modifying my .pro file made all the difference.
But now I had to download SIP and PyQT. I followed the docs on there. There are a few more problems. Follow the links or the directions which are left there in case the information is removed.
If your SIP make install has an error where it is looking at Unix paths (/usr/bin) instead of DOS paths (C:\QT), look at this link http://old.nabble.com/Building-SIP-on-MinGW-:-problem-at-%22make-install%22-td28909249.html#
(short version: the problem is the sh.exe in one of your other linux compilers like cygwin or msys, change the name temporarily to force the make install to use DOS path naming):
If you configure PyQT and it spits out a file error that has to do with QTCore
Google pexports and download. Go to %QTdir%/bin. Then follow instructions or link ( http://jeethurao.com/blog/?p=18 )
pexports QtCore4.dll > QtCore4.def
dlltool –dllname QtCore4.dll –def QtCore4.def –output-lib libQtCore4.a
move libQtCore4.a ..\lib
And now you know kung-fu.
P.S: I never tried this method myself. This is a different, but untested (by me) method of compiling PyQT, done up by the trolls at Trolltech:
http://www.diotavelli.net/PyQtWiki/InstallingPyQTCommercialWin