[ANNOUNCEMENT] Updated: python3-h5py-2.5.0-1
Version 2.5.0-1 of python3-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. This version of python3-h5py has been built with the latest version of HDF5 (1.8.15-1) and includes the following changes: HDF5 for Python (h5py) 2.0 represents the first major refactoring of the h5py codebase since the project’s launch in 2008. Many of the most important changes are behind the scenes, and include changes to the way h5py interacts with the HDF5 library and Python. These changes have substantially improved h5py’s stability, and make it possible to use more modern versions of HDF5 without compatibility concerns. It is now also possible to use h5py with Python 3. For a complete list of changes, please see http://docs.h5py.org/en/latest/whatsnew/2.0.html. This version was built without parallel I/O support and does not use MPI. Cython is a build requirement, which is available on Cygwinports. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[ANNOUNCEMENT] Updated: python-h5py-2.5.0-1
Version 2.5.0-1 of python-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. This version of python-h5py has been built with the latest version of HDF5 (1.8.15-1) and includes the following changes: HDF5 for Python (h5py) 2.0 represents the first major refactoring of the h5py codebase since the project’s launch in 2008. Many of the most important changes are behind the scenes, and include changes to the way h5py interacts with the HDF5 library and Python. These changes have substantially improved h5py’s stability, and make it possible to use more modern versions of HDF5 without compatibility concerns. It is now also possible to use h5py with Python 3. For a complete list of changes, please see http://docs.h5py.org/en/latest/whatsnew/2.0.html. This version was built without parallel I/O support and does not use MPI. Cython is a build requirement, which is available on Cygwinports. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[ANNOUNCEMENT] [ANNOUNCEMENT] Updated: python3-h5py-2.4.0-1
Version 2.4.0-1 of python3-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. This version of python3-h5py has been built with the latest version of HDF5 (1.8.14) and includes the following changes: This release incorporates a total re-write of the identifier management system in h5py. As part of this refactoring, the entire API is also now protected by threading locks. User-visible changes include: Files are now automatically closed when all objects within them are unreachable. Previously, if File.close() was not explicitly called, files would remain open and "leaks" were possible if the File object was lost. The entire API is now believed to be thread-safe (feedback welcome!). External links now work if the target file is already open. Previously this was not possible because of a mismatch in the file close strengths. The options to setup.py have changed; a new top-level "configure" command handles options like --hdf5=/path/to/hdf5 and --mpi. Setup.py now works correctly under Python 3 when these options are used. Cython (0.17+) is now required when building from source. The minimum NumPy version is now 1.6.1. Various other enhancements and bug fixes This version was built without parallel I/O support and does not use MPI. Cython is now a build requirement, which is available on Cygwinports. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[ANNOUNCEMENT] [ANNOUNCEMENT] Updated: python-h5py-2.4.0-1
Version 2.4.0-1 of python-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. This version of python-h5py has been built with the latest version of HDF5 (1.8.14) and includes the following changes: This release incorporates a total re-write of the identifier management system in h5py. As part of this refactoring, the entire API is also now protected by threading locks. User-visible changes include: Files are now automatically closed when all objects within them are unreachable. Previously, if File.close() was not explicitly called, files would remain open and "leaks" were possible if the File object was lost. The entire API is now believed to be thread-safe (feedback welcome!). External links now work if the target file is already open. Previously this was not possible because of a mismatch in the file close strengths. The options to setup.py have changed; a new top-level "configure" command handles options like --hdf5=/path/to/hdf5 and --mpi. Setup.py now works correctly under Python 3 when these options are used. Cython (0.17+) is now required when building from source. The minimum NumPy version is now 1.6.1. Various other enhancements and bug fixes This version was built without parallel I/O support and does not use MPI. Cython is now a build requirement, which is available on Cygwinports. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[ANNOUNCEMENT] Updated: python3-h5py-2.3.1-1
Version 2.3.1-1 of python3-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. This version of python3-h5py has been built with the latest version of HDF5 (1.8.13) to fix HDF5 library version errors seen when the Cygwin hdf5 package was updated. It also includes upstream bugfixes for the MPIPOSIX driver and Travis-CI issues. This version was built without parallel I/O support and does not use MPI. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[ANNOUNCEMENT] Updated: python-h5py-2.3.1-1
Version 2.3.1-1 of python-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. This version of python-h5py has been built with the latest version of HDF5 (1.8.13) to fix HDF5 library version errors seen when the Cygwin hdf5 package was updated. It also includes upstream bugfixes for the MPIPOSIX driver and Travis-CI issues. This version was built without parallel I/O support and does not use MPI. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[ANNOUNCEMENT] New package: python3-h5py-2.2.1-1
Version 2.2.1-1 of python3-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax. For example, you can iterate over datasets in a file, or check out the .shape or .dtype attributes of datasets. You don't need to know anything special about HDF5 to get started. In addition to the easy-to-use high level interface, h5py rests on a object-oriented Cython wrapping of the HDF5 C API. Almost anything you can do from C in HDF5, you can do from h5py. Best of all, the files you create are in a widely-used standard binary format, which you can exchange with other people, including those who use programs like IDL and MATLAB. This version was built for Python 3 without support for the parallel I/O features introduced in version 2.2.0. For more information please visit http://www.h5py.org. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[ANNOUNCEMENT] New package: python-h5py-2.2.1-1
Version 2.2.1-1 of python-h5py has been uploaded for both x86 and x86_64. The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax. For example, you can iterate over datasets in a file, or check out the .shape or .dtype attributes of datasets. You don't need to know anything special about HDF5 to get started. In addition to the easy-to-use high level interface, h5py rests on a object-oriented Cython wrapping of the HDF5 C API. Almost anything you can do from C in HDF5, you can do from h5py. Best of all, the files you create are in a widely-used standard binary format, which you can exchange with other people, including those who use programs like IDL and MATLAB. This version was built without support for the parallel I/O features introduced in version 2.2.0. For more information please visit http://www.h5py.org. *** CYGWIN-ANNOUNCE UNSUBSCRIBE INFO *** If you want to unsubscribe from the cygwin-announce mailing list, look at the "List-Unsubscribe: " tag in the email header of this message. Send email to the address specified there. It will be in the format: cygwin-announce-unsubscribe-you=yourdomain.com cygwin.com If you need more information on unsubscribing, start reading here: http://sourceware.org/lists.html#unsubscribe-simple Please read *all* of the information on unsubscribing that is available starting at this URL. -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
possible missing dependency for python-numpy and proposed fix
Hi, I recently installed a new version of Cygwin on a new Windows 7 machine. I installed a several packages including numpy. The installation worked without any errors. I did this for both 32 and 64 bit versions of Cygwin. After installing numpy I tried importing it in a Python shell. It raised an ImportError exception when trying to import lapack_lite. Lapack_lite.dll existed in the correct location, but running "cygcheck -c" (as per http://cygwin.com/ml/cygwin/2013-05/msg00361.html) on it revealed that it needed libquadmath0 which had not been installed. Numpy worked fine once I installed the missing libquadmath0 dependency. Is anyone else seeing this problem? Should this dependency be added to the numpy setup.hint? Cheers, Chris LeBlanc -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
[1.7] Use of SSH public/private keys requires administrator rights
Hello, I seem to have found a bug with SSH under Cygwin 1.7 (beta). Luckily I also found a workaround as I was writing this email, which is near the bottom. I've installed Cygwin 1.7 yesterday using the normal setup.exe method for all users on the system, and installing a few extra packages (gcc, subversion, make, some other dev tools) including openssh. I've run "ssh-host-config" (using CYGWIN="ntsec tty", and answering all other questions with yes) and "cygserver-config" to run both of these as services, no other services have been started. If I ssh from any other machine (including the Cygwin server) to the Cygwin server, it will connect without any problems. I can run a command on the remote machine such as "ssh cygwin_machine hostname", I can also use sftp, and rsync over ssh to transfer files. This all sounds good, and everything is working at this point. However, if I setup SSH keys using ssh-keygen to allow ssh-ing without passwords, I start to run into problems. I can ssh from to the Cygwin ssh server, but if I try to run the command "ssh cygwin_machine hostname" or transfer files using rsync over ssh, it will raise an error. Sftp will simply close the connection immediately. I already had an existing SSH public key, but this is how it was created quite some time ago. cd ~/.ssh ssh-keygen -t dsa(no pass phrases) On Cygwin server: copy id_dsa.pub from original host to ~/.ssh/authorized_keys on Cygwin machine chmod 600 authorized_keys Here are the errors I get when I try to login from a remote machine (typically Linux) as the same user. The account on the windows machine is the default type of user, not an Administrator. >From the command "ssh cygwin_machine hostname", error: 7 [main] sshd 720 C:\cygwin\usr\sbin\sshd.exe: *** fatal error - could not load user32, Win32 error 1114 >From the command "rsync -ave ssh localdir/ cygwin_machine:/tmp/remotedir" 7 [main] sshd 768 C:\cygwin\usr\sbin\sshd.exe: *** fatal error - could not load user32, Win32 error 1114 rsync: connection unexpectedly closed (0 bytes received so far) [sender] rsync error: error in rsync protocol data stream (code 12) at io.c(434) >From the command "sftp cygwin_machine": Connecting to cygwin_machine... Connection closed The /var/log/sshd.log file is empty. Cygcheck show OpenSSH is at version 5.2p1-4, and Cygwin is at version 1.7.0-59, and all packages are OK. Here is the workaround: As part of debugging this problem, I tried creating new ssh keys under Cygwin for the Administrator user. I then copied id_dsa.pub to authorized_keys, which should allow password-less SSHing on localhost (eg: the command "ssh localhost" won't require a password when run on the Cygwin machine under the Administrator account). Interestingly, this worked without any of the errors above. I then tried modifying the rights of the normal user I had been using, changing them to be an administrator using the standard Windows "Users and passwords" tool. I also ran "mkpasswd -l > /etc/passwd" and "mkgroup -l > /etc/group" to remake these files, just in case. Suddenly ssh, sftp, and rsync over ssh are now working fine for this user. This was a pretty difficult problem to find. I'm not sure if its a bug or a feature, I'm guessing a bug. Perhaps this workaround should be added to the FAQ. Cheers, Chris -- Chris LeBlanc Claritas Development GNS Science -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
Re: problems using Xlib.h/Xwindows.h/unistd.h and win32api under gcc-4
Hi Dave, Thanks for the description of the problem, and the workaround. Our code is pretty complicated at points, so it might be challenging to be sure of the include order, but I'll try. The other suggestion I saw from Christopher Faylor was to try Cygwin commercial support. This was actually the first major problem I've had with Cygwin, so I haven't had to use it before and didn't even think of it. I'll try contacting them tomorrow, and possibly get a fix for the strange looking defines in Xwindows.h, so the order of includes shouldn't matter. Personally, I'd be happy with sleep() being defined in unistd.h, and Sleep() defined in Windows.h, and keeping the two separate. Thanks again for your help, Chris -- Chris LeBlanc Claritas Development GNS Science Lower Hutt, New Zealand Web: www.globeclaritas.com -- Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple Problem reports: http://cygwin.com/problems.html Documentation: http://cygwin.com/docs.html FAQ: http://cygwin.com/faq/
problems using Xlib.h/Xwindows.h/unistd.h and win32api under gcc-4
Hi,
I'm trying to migrate our commercial software (we've purchased a
commercial Cygwin license) thats been running well on Cygwin using gcc
3.x to gcc-4. Its mature Unix/Linux C and Fortran code. We're using
the win32api so we can use native Windows file dialogs. This has been
working in gcc 3.4, but now raises an error with gcc 4.3.2 (updated
Cygwin yesterday). I've narrowed this down with a bit of example
code:
#include
/* The next two includes have conflicts: */
#include
#include
/* so do these two: */
//#include
#include
int main() {
printf("Hello\n");
return 0;
}
This ultra-simple program includes ,
(win32api), and unistd.h. I gave gcc-4 the flags -lX11 for X11
libraries, and -lcomdlg32 for the Windows dialog libraries. Here is
the error I see:
> gcc-4 test_sleep.c -Wall -lX11 -lcomdlg32 -o test_sleep
In file included from
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/windows.h:87,
from test_sleep.c:5:
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/winspool.h:255:
error: two or more data types in declaration specifiers
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/winspool.h:270:
error: two or more data types in declaration specifiers
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/winspool.h:291:
error: two or more data types in declaration specifiers
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/winspool.h:316:
error: two or more data types in declaration specifiers
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/winspool.h:571:
error: two or more data types in declaration specifiers
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/winspool.h:594:
error: two or more data types in declaration specifiers
I noticed this post:
http://sourceware.org/ml/cygwin/2009-03/msg00420.html, so tried
replacing with . This now raises a
different error, this time conflicting with unistd.h. If we also
comment out the include for windows.h, we still get the same error:
> gcc-4 test_sleep.c -Wall -lX11 -lcomdlg32 -o test_sleep
In file included from /usr/include/unistd.h:4,
from test_sleep.c:4:
/usr/include/sys/unistd.h:144: error: expected declaration specifiers
or '...' before '(' token
/usr/include/sys/unistd.h:144: error: conflicting types for 'Sleep'
/usr/lib/gcc/i686-pc-cygwin/4.3.2/../../../../include/w32api/winbase.h:1984:
error: previous declaration of 'Sleep' was here
So in summary, X11/Xlib.h conflicts with windows.h, and X11/Xwindow.h
conflicts with unistd.h.
Any suggestions on how to get around this (unfortunately I need
unistd.h, windows.h, and either Xlib.h or Xwindows.h)? The fact that
Xwindows.h conflicts with unistd.h (a common scenario) suggests a bug
in Xwindows.h, unfortunately I'm not sure how to fix the problem.
Cheers,
Chris
--
Chris LeBlanc
Claritas Development
GNS Science
Lower Hutt, New Zealand
Web: www.globeclaritas.com
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