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pyrap.measures not correctly linked with casacore2-dev 2.2.0-2kern1 in python-casacore 2.1.2

casacore 2.2.0-2kern1 installed:

sperkins@simon-Y700:~$ apt show casacore-dev
Package: casacore-dev
Version: 2.2.0-2kern1
Priority: optional
Section: libdevel
Source: casacore
Maintainer: Debian Astronomy & Astrophysics Maintainers <[email protected]>
Installed-Size: 12.9 MB
Depends: libcasa-casa2 (= 2.2.0-2kern1), libcasa-coordinates2 (= 2.2.0-2kern1), libcasa-derivedmscal2 (= 2.2.0-2kern1), libcasa-fits2 (= 2.2.0-2kern1), libcasa-images2 (= 2.2.0-2kern1), libcasa-lattices2 (= 2.2.0-2kern1), libcasa-meas2 (= 2.2.0-2kern1), libcasa-measures2 (= 2.2.0-2kern1), libcasa-mirlib2 (= 2.2.0-2kern1), libcasa-ms2 (= 2.2.0-2kern1), libcasa-msfits2 (= 2.2.0-2kern1), libcasa-python2 (= 2.2.0-2kern1), libcasa-scimath-f2 (= 2.2.0-2kern1), libcasa-scimath2 (= 2.2.0-2kern1), libcasa-tables2 (= 2.2.0-2kern1)
Download-Size: 1,522 kB
APT-Manual-Installed: yes
APT-Sources: http://ppa.launchpad.net/kernsuite/kern-dev/ubuntu xenial/main amd64 Packages
Description: CASA core library development files
 The casacore package contains the core libraries of the old
 AIPS++/CASA (Common Astronomy Software Applications) package. This
 split was made to get a better separation of core libraries and
 applications.
 .
 This package contains the files for application development.

Create and activate a virtual environment

sperkins@simon-Y700:~$ virtualenv venv/pyrap
New python executable in /home/sperkins/venv/pyrap/bin/python
Installing setuptools, pip, wheel...done.
sperkins@simon-Y700:~$ source ~/venv/pyrap/bin/activate
(pyrap) sperkins@simon-Y700:~$ pip install python-casacore
Collecting python-casacore
Collecting numpy (from python-casacore)
  Using cached numpy-1.12.0-cp27-cp27mu-manylinux1_x86_64.whl
Requirement already satisfied: setuptools in ./venv/pyrap/lib/python2.7/site-packages (from python-casacore)
Requirement already satisfied: appdirs>=1.4.0 in ./venv/pyrap/lib/python2.7/site-packages (from setuptools->python-casacore)
Requirement already satisfied: packaging>=16.8 in ./venv/pyrap/lib/python2.7/site-packages (from setuptools->python-casacore)
Requirement already satisfied: six>=1.6.0 in ./venv/pyrap/lib/python2.7/site-packages (from setuptools->python-casacore)
Requirement already satisfied: pyparsing in ./venv/pyrap/lib/python2.7/site-packages (from packaging>=16.8->setuptools->python-casacore)
Installing collected packages: numpy, python-casacore
Successfully installed numpy-1.12.0 python-casacore-2.1.2

Try to import `pyrap.measures`

(pyrap) sperkins@simon-Y700:~$ python -c 'import pyrap.measures'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/sperkins/venv/pyrap/local/lib/python2.7/site-packages/pyrap/measures.py", line 1, in <module>
    from casacore.measures import *
  File "/home/sperkins/venv/pyrap/local/lib/python2.7/site-packages/casacore/measures/__init__.py", line 30, in <module>
    import casacore.quanta as dq
  File "/home/sperkins/venv/pyrap/local/lib/python2.7/site-packages/casacore/quanta/__init__.py", line 1, in <module>
    from .quantity import quantity, is_quantity
  File "/home/sperkins/venv/pyrap/local/lib/python2.7/site-packages/casacore/quanta/quantity.py", line 2, in <module>
    from ._quanta import Quantity
ImportError: /home/sperkins/venv/pyrap/local/lib/python2.7/site-packages/casacore/quanta/_quanta.so: undefined symbol: _ZN4casa16throwArrayShapesEPKc
(pyrap) sperkins@simon-Y700:~$

T2runtime missing?

After installing tempo2 (sudo apt-get install tempo2), the environment variable $TEMPO2 does not get set automatically, which I guess is fair enough. It is supposed to point to the T2runtime directory, which I could not locate as being install somewhere when install the package. I have just missed it? As a quick fix, I have downloaded the tempo2 source code from its github repo as it contains the T2runtime folder, and then pointed the environment variable to it. Perhaps this needs fixing? Or maybe it is just that it's at an location unknown from me?

I wondering if it might not be good having a some page when a list of environment variables which one should set after install specific packages be made?

casacore 2.2.0 in KERN-dev expects casacore data in wrong location

21cmFAST simulation packaging

Hi Gijs,
Can you please package these 21-cm simulations.

21cmFAST : https://github.com/andreimesinger/21cmFAST

Simfast21 : https://github.com/mariogrs/Simfast21

With Thanks,
Abhik

package up pulsar software

http://www.ljtwebdevelopment.com/pulsarref/

libcasa_msvis.so error in lwimager, awimager, meqserver

I installed lofar and meqtrees-timba using kerne-1 ppa in Ubuntu 16.04.2. Other software like wsclean, aoflagger worked. but getting the following errors while trying to run 3 packages:

lwimager
lwimager: error while loading shared libraries: libcasa_msvis.so: cannot open shared object file: No such file or directory
awimager
awimager: error while loading shared libraries: libcasa_msvis.so: cannot open shared object file: No such file or directory
meqserver
meqserver: error while loading shared libraries: libcasa_msvis.so: cannot open shared object file: No such file or directory

Because of this meqserver problem, cannot start a server in meqbrowser.

add CASA package

We can actually just make a deb package of casa, but it won't integrate nicely with for example the system python.

Recipies for a few packages

Okay so per conversation earlier we could theoretically create debian packages for a few more packages. These are the docker recipes I've made for 3GCIV (a bit patchy but all there):
https://github.com/bennahugo/3GCIV_Docker

There is also a fix in there for the NRAO CASA docker image. With the help of Eric Greisen and Tom Mauch I've got AIPS along with the TV going as well. The .bashrc contains the lines necessary to run these packages with X11 support.

Add montage?

Is it possible to add montage again to the kernsuite?

pybdsm isn't correctly installed with the lofar package

After adding the KERN-1 repo, and installing the lofar package using apt-get install lofar, the pybdsm program doesn't work.

When I try to run it, it says

/usr/bin/python: can't open file '/usr/lib/python2.7/site-packages/lofar/bdsm/pybdsm.py': [Errno 2] No such file or directory

The executable at /usr/bin/pybdsm seems to point to the above location, but the folder site-packages doesn't exist under /usr/lib/python2.7, but it does exist (and is empty) at /usr/local/lib/python2.7.

Running locate lofar doesn't seem to throw up anything either, even after a reboot.

Update wsclean to 2.3

Could wsclean on kern-dev be updated to 2.3 please?

python-presto conflicts with python-ppgplot

Unpacking python-presto (2+git20160604-1kern6) ...
dpkg: error processing archive /var/cache/apt/archives/python-presto_2+git20160604-1kern6_amd64.deb (--unpack):
 trying to overwrite '/usr/lib/python2.7/dist-packages/ppgplot/__init__.py', which is also in package python-ppgplot 1.4-3trusty

issue installing psrchive package

hi! thanks for making such an awesome project! it was awesome i'm so happy.

but there is this problem when i install the psrchive package:

ina@neiman:~$ sudo apt-get install psrchive
[sudo] password for nina: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  psrchive
0 upgraded, 1 newly installed, 0 to remove and 79 not upgraded.
Need to get 0 B/30,2 MB of archives.
After this operation, 247 MB of additional disk space will be used.
(Reading database ... 423367 files and directories currently installed.)
Preparing to unpack .../psrchive_2012.12+20160608-1_amd64.deb ...
Unpacking psrchive (2012.12+20160608-1) ...
dpkg: error processing archive /var/cache/apt/archives/psrchive_2012.12+20160608-1_amd64.deb (--unpack):
 trying to overwrite '/usr/include/debug.h', which is also in package dspsr 0+git20160608-1kern1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Errors were encountered while processing:
 /var/cache/apt/archives/psrchive_2012.12+20160608-1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

thanks you!

'~kernsuite' user or team does not exist.

I am trying to install casacore on ubuntu 16.04 and for the past week and everytime I add the repository i keep getting the error:
Cannot add PPA: 'ppa:~kernsuite/ubuntu/kern-2'.
ERROR: '~kernsuite' user or team does not exist.
Is it possible that your servers have been down recently or maybe I am doing something wrong?.

casacore build flags (ENABLE_TABLELOCKING)

I ran into an issue with casacore that I suspect is related to the Lustre filesystem on the cluster I'm using (see https://www.astron.nl/lofarwiki/doku.php?id=public:install_lofar_centos6.5, 3.2 casacore for why I suspect Lustre). The error I get when running NDPPP is:

terminate called after throwing an instance of 'casa::TableError'
  what():  Error (Function not implemented) when acquiring lock on /data/working_L531971/pipeline/L531971_SB470_uv.calibrator-flagcal/table.lock

Based on the information in the link above, casacore table locking doesn't play nice with Lustre. My question is whether there's any way to turn off table locking when installing casacore via Kern (or after installing). I am very hesitant to try installing from source and invoking that build option because I don't want to mess up everything that depends on casacore. Is doing a build from source the only option? Is there any way that build options like -DENABLE_TABLELOCKING=NO can be accessed when installing a Kern module via apt-get?

FWIW, I'm running casacore/NDPPP/genericpipeline/etc. from a Singularity container I built and maintain myself. It has worked on other single node machines, but threw the error above when I tried running it on data stored on a Lustre filesystem.

slack integration test

add binary version for dependencies to packages, just like casacore package

Can't see blockio.h while pip install python-casacore in virtualenv

pip falls over while installing python-casacore in virtualenv. Here is my output

pip install python-casacore
Collecting python-casacore
Using cached python-casacore-2.1.2.tar.gz
Requirement already satisfied: numpy in ./lib/python2.7/site-packages (from python-casacore)
Requirement already satisfied: setuptools in ./lib/python2.7/site-packages (from python-casacore)
Requirement already satisfied: appdirs>=1.4.0 in ./lib/python2.7/site-packages (from setuptools->python-casacore)
Requirement already satisfied: packaging>=16.8 in ./lib/python2.7/site-packages (from setuptools->python-casacore)
Requirement already satisfied: six>=1.6.0 in ./lib/python2.7/site-packages (from setuptools->python-casacore)
Requirement already satisfied: pyparsing in ./lib/python2.7/site-packages (from packaging>=16.8->setuptools->python-casacore)
Building wheels for collected packages: python-casacore
Running setup.py bdist_wheel for python-casacore ... error
Complete output from command /home/landman/virtualenvs/mb/bin/python2 -u -c "import setuptools, tokenize;file='/tmp/pip-build-Uu5gao/python-casacore/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/tmpu9v3Kipip-wheel- --python-tag cp27:
Warning: could not find casa library dir for dependency tracking.
Possibly not rebuilding. Specify --force to force a rebuild.
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/pyrap
copying pyrap/images.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/quanta.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/functionals.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/tables.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/measures.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/fitting.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/init.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/util.py -> build/lib.linux-x86_64-2.7/pyrap
creating build/lib.linux-x86_64-2.7/casacore
copying casacore/six.py -> build/lib.linux-x86_64-2.7/casacore
copying casacore/init.py -> build/lib.linux-x86_64-2.7/casacore
creating build/lib.linux-x86_64-2.7/pyrap/images
copying pyrap/images/image.py -> build/lib.linux-x86_64-2.7/pyrap/images
copying pyrap/images/init.py -> build/lib.linux-x86_64-2.7/pyrap/images
copying pyrap/images/coordinates.py -> build/lib.linux-x86_64-2.7/pyrap/images
creating build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tablerow.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tableiter.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/table.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/wxtablebrowser.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tableindex.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tablecolumn.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tablehelper.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/msutil.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tableutil.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/init.py -> build/lib.linux-x86_64-2.7/casacore/tables
creating build/lib.linux-x86_64-2.7/casacore/images
copying casacore/images/image.py -> build/lib.linux-x86_64-2.7/casacore/images
copying casacore/images/init.py -> build/lib.linux-x86_64-2.7/casacore/images
copying casacore/images/coordinates.py -> build/lib.linux-x86_64-2.7/casacore/images
creating build/lib.linux-x86_64-2.7/casacore/functionals
copying casacore/functionals/functional.py -> build/lib.linux-x86_64-2.7/casacore/functionals
copying casacore/functionals/init.py -> build/lib.linux-x86_64-2.7/casacore/functionals
creating build/lib.linux-x86_64-2.7/casacore/util
copying casacore/util/substitute.py -> build/lib.linux-x86_64-2.7/casacore/util
copying casacore/util/init.py -> build/lib.linux-x86_64-2.7/casacore/util
creating build/lib.linux-x86_64-2.7/casacore/fitting
copying casacore/fitting/fitting.py -> build/lib.linux-x86_64-2.7/casacore/fitting
copying casacore/fitting/init.py -> build/lib.linux-x86_64-2.7/casacore/fitting
creating build/lib.linux-x86_64-2.7/casacore/measures
copying casacore/measures/init.py -> build/lib.linux-x86_64-2.7/casacore/measures
creating build/lib.linux-x86_64-2.7/casacore/quanta
copying casacore/quanta/quantity.py -> build/lib.linux-x86_64-2.7/casacore/quanta
copying casacore/quanta/init.py -> build/lib.linux-x86_64-2.7/casacore/quanta
running build_ext
building 'casacore.fitting._fitting' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/fit.cc -o build/temp.linux-x86_64-2.7/src/fit.o
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/fitting.cc -o build/temp.linux-x86_64-2.7/src/fitting.o
c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/src/fit.o build/temp.linux-x86_64-2.7/src/fitting.o -lcasa_scimath -lcasa_scimath_f -lboost_python-py27 -lcasa_python -o build/lib.linux-x86_64-2.7/casacore/fitting/_fitting.so
building 'casacore.functionals._functionals' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/functional.cc -o build/temp.linux-x86_64-2.7/src/functional.o
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/functionals.cc -o build/temp.linux-x86_64-2.7/src/functionals.o
c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/src/functional.o build/temp.linux-x86_64-2.7/src/functionals.o -lcasa_scimath -lcasa_scimath_f -lboost_python-py27 -lcasa_python -o build/lib.linux-x86_64-2.7/casacore/functionals/_functionals.so
building 'casacore.images._images' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/images.cc -o build/temp.linux-x86_64-2.7/src/images.o
In file included from /usr/include/casacore/fits/FITS/hdu.h:33:0,
from /usr/include/casacore/images/Images/FITS2Image.tcc:38,
from /usr/include/casacore/images/Images/FITSImage.h:329,
from src/images.cc:36:
/usr/include/casacore/fits/FITS/blockio.h:35:50: fatal error: fitsio.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Failed building wheel for python-casacore
Running setup.py clean for python-casacore
Failed to build python-casacore
Installing collected packages: python-casacore
Running setup.py install for python-casacore ... error
Complete output from command /home/landman/virtualenvs/mb/bin/python2 -u -c "import setuptools, tokenize;file='/tmp/pip-build-Uu5gao/python-casacore/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-8llxhb-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/landman/virtualenvs/mb/include/site/python2.7/python-casacore:
Warning: could not find casa library dir for dependency tracking.
Possibly not rebuilding. Specify --force to force a rebuild.
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/pyrap
copying pyrap/images.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/quanta.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/functionals.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/tables.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/measures.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/fitting.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/init.py -> build/lib.linux-x86_64-2.7/pyrap
copying pyrap/util.py -> build/lib.linux-x86_64-2.7/pyrap
creating build/lib.linux-x86_64-2.7/casacore
copying casacore/six.py -> build/lib.linux-x86_64-2.7/casacore
copying casacore/init.py -> build/lib.linux-x86_64-2.7/casacore
creating build/lib.linux-x86_64-2.7/pyrap/images
copying pyrap/images/image.py -> build/lib.linux-x86_64-2.7/pyrap/images
copying pyrap/images/init.py -> build/lib.linux-x86_64-2.7/pyrap/images
copying pyrap/images/coordinates.py -> build/lib.linux-x86_64-2.7/pyrap/images
creating build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tablerow.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tableiter.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/table.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/wxtablebrowser.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tableindex.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tablecolumn.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tablehelper.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/msutil.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/tableutil.py -> build/lib.linux-x86_64-2.7/casacore/tables
copying casacore/tables/init.py -> build/lib.linux-x86_64-2.7/casacore/tables
creating build/lib.linux-x86_64-2.7/casacore/images
copying casacore/images/image.py -> build/lib.linux-x86_64-2.7/casacore/images
copying casacore/images/init.py -> build/lib.linux-x86_64-2.7/casacore/images
copying casacore/images/coordinates.py -> build/lib.linux-x86_64-2.7/casacore/images
creating build/lib.linux-x86_64-2.7/casacore/functionals
copying casacore/functionals/functional.py -> build/lib.linux-x86_64-2.7/casacore/functionals
copying casacore/functionals/init.py -> build/lib.linux-x86_64-2.7/casacore/functionals
creating build/lib.linux-x86_64-2.7/casacore/util
copying casacore/util/substitute.py -> build/lib.linux-x86_64-2.7/casacore/util
copying casacore/util/init.py -> build/lib.linux-x86_64-2.7/casacore/util
creating build/lib.linux-x86_64-2.7/casacore/fitting
copying casacore/fitting/fitting.py -> build/lib.linux-x86_64-2.7/casacore/fitting
copying casacore/fitting/init.py -> build/lib.linux-x86_64-2.7/casacore/fitting
creating build/lib.linux-x86_64-2.7/casacore/measures
copying casacore/measures/init.py -> build/lib.linux-x86_64-2.7/casacore/measures
creating build/lib.linux-x86_64-2.7/casacore/quanta
copying casacore/quanta/quantity.py -> build/lib.linux-x86_64-2.7/casacore/quanta
copying casacore/quanta/init.py -> build/lib.linux-x86_64-2.7/casacore/quanta
running build_ext
building 'casacore.fitting._fitting' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/fit.cc -o build/temp.linux-x86_64-2.7/src/fit.o
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/fitting.cc -o build/temp.linux-x86_64-2.7/src/fitting.o
c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/src/fit.o build/temp.linux-x86_64-2.7/src/fitting.o -lcasa_scimath -lcasa_scimath_f -lboost_python-py27 -lcasa_python -o build/lib.linux-x86_64-2.7/casacore/fitting/_fitting.so
building 'casacore.functionals._functionals' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/functional.cc -o build/temp.linux-x86_64-2.7/src/functional.o
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/functionals.cc -o build/temp.linux-x86_64-2.7/src/functionals.o
c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/src/functional.o build/temp.linux-x86_64-2.7/src/functionals.o -lcasa_scimath -lcasa_scimath_f -lboost_python-py27 -lcasa_python -o build/lib.linux-x86_64-2.7/casacore/functionals/_functionals.so
building 'casacore.images._images' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/images.cc -o build/temp.linux-x86_64-2.7/src/images.o
In file included from /usr/include/casacore/fits/FITS/hdu.h:33:0,
from /usr/include/casacore/images/Images/FITS2Image.tcc:38,
from /usr/include/casacore/images/Images/FITSImage.h:329,
from src/images.cc:36:
/usr/include/casacore/fits/FITS/blockio.h:35:50: fatal error: fitsio.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

----------------------------------------

Command "/home/landman/virtualenvs/mb/bin/python2 -u -c "import setuptools, tokenize;file='/tmp/pip-build-Uu5gao/python-casacore/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-8llxhb-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/landman/virtualenvs/mb/include/site/python2.7/python-casacore" failed with error code 1 in /tmp/pip-build-Uu5gao/python-casacore/

I have all of casacore-{data,dev,tools} installed as well as wcslib-{dev,tools} and have checked that the file /usr/include/casacore/fits/FITS/blockio.h exists. This doesn't happen when I pip install python-casacore outside virtualenv. What am I missing?

tempo2 inviroment variable doesn't work

I'm trying to run tempo2 from outside docker but it didn't work.
Environment variable >TEMPO2< not set
and
I can't find tempo2 observatories.dat and "running directory"
PSRCAT: Unable to open catalogue file: /pulsar/psr/runtime/psrcat/psrcat.db

Regards,

backport pyqwt >= 5.2.1~cvs20091107+dfsg-8

meqtrees doesn't work at the moment, it requires a fixed numpy.

ratt-ru/meqtrees#860

https://tracker.debian.org/pkg/pyqwt5

https://anonscm.debian.org/git/python-modules/packages/pyqwt5.git/commit/?id=e22e7e1ce7b78ef83edd438d91e137aa4ce17807

SPAM

Hi Gijs,
Can you please package SPAM (the help page to install SPAM is here https://safe.nrao.edu/wiki/bin/view/Main/HuibIntemaSpamInstall) so that it can be used in stimela. Thanks.

Cheers,
Abhik

chgcentre tool

Phase rotates a given Measurement Set. Linked to wsclean, but not available (at least on jake/elwood). Would be be very useful to have it included in Kern.

https://sourceforge.net/p/wsclean/wiki/chgcentre/

Could you please package SoFiA

https://github.com/SoFiA-Admin/SoFiA

attrdict package is missing python dependency

https://launchpad.net/~kernsuite/+archive/ubuntu/kern-dev/+build/11985378/+files/buildlog_ubuntu-xenial-amd64.attrdict_2.0.0-1_BUILDING.txt.gz

update to lofar 2.17.3 when released

DPPP in 2.17.3 contains a serious bug, it would be nice if lofar 2.17.3 made it in kern-1

libtempo2pred.so.0 missing

I have installed tempo2 (sudo apt-get install tempo2) and after fixing the (possible) issue with the missing T2runtime directory ( #48 ) it works fine.

I have then installed the psrchive suite (sudo apt-get install psrchive). When attempting to run one of its programmes (pav -h) it crashes with the following error: pav: error while loading shared libraries: libtempo2pred.so.0: cannot open shared object file: No such file or directory.

It appears that the tempo2 libraries are missing. The environment variable $LD_LIBRARY_PATH is not set and this possibly needs to be done. However I could not locate the missing library anywhere.

Any clue?

building SOPT 2.0.0-1 package for ubuntu 16.04 fails

CMake Error at cmake_files/dependencies.cmake:3 (find_package):
  By not providing "Findspdlog.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "spdlog", but
  CMake did not find one.

  Could not find a package configuration file provided by "spdlog" with any
  of the following names:

    spdlogConfig.cmake
    spdlog-config.cmake

  Add the installation prefix of "spdlog" to CMAKE_PREFIX_PATH or set
  "spdlog_DIR" to a directory containing one of the above files.  If "spdlog"
  provides a separate development package or SDK, be sure it has been
  installed.
Call Stack (most recent call first):
  CMakeLists.txt:35 (include)


-- Configuring incomplete, errors occurred!

Tigger 1.3.4 fails to load fits files

Tigger 1.3.4 gives me this error whenever I try to load a fits file (which other image viewers load normally)

Error loading FITS image 1466813419_1284.hh_vv.ms_1-7_fixed.ms_I_3deg_pself1.image.fits: 'Header' object has no attribute 'ascard'. This may be due to a bug in Tigger; if the FITS file loads fine in another viewer, please send the FITS file, along with a copy of any error messages from the text console, to [email protected].

The traceback on the terminal shows this

File "/usr/lib/python2.7/dist-packages/Tigger/Images/Manager.py", line 128, in loadImage
image = SkyImage.FITSImagePlotItem(str(filename));
File "/usr/lib/python2.7/dist-packages/Tigger/Images/SkyImage.py", line 553, in init
self.read(filename,hdu);
File "/usr/lib/python2.7/dist-packages/Tigger/Images/SkyImage.py", line 581, in read
hdr1 = pyfits.Header(filter(lambda x:not str(x).startswith('HISTORY'),hdr.ascard));
AttributeError: 'Header' object has no attribute 'ascard'

I have not seen this issue on the same version of tigger on ubuntu 14.04

sigproc and presto are in conflict in kern-1

dpkg: error processing archive /var/cache/apt/archives/sigproc_0.0+git20150224-1_amd64.deb (--unpack):
trying to overwrite '/usr/bin/downsample', which is also in package presto 2+git20160604-1kern6
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)

package up ScatterBrane

https://github.com/krosenfeld/scatterbrane

hi! sphe here! can you please package this package? please

https://github.com/SpheMakh/msutils

this one please yes please

PRESTO dependencies

PRESTO uses TEMPO for many routines. Maybe add this as a dependency?
It also include some python2 routines. The most used ones require at least numpy, scipy & matplotlib. Also make sure that python can find the routines, they're in /usr/lib/python now.

TEMPO needs some files that are missing

TEMPO needs some configuration files and directories: tempo.hlp, tempo.cfg and the dirs referenced in the cfg file. These need to be located in the $TEMPO directory.

add lofar dependency to wsclean

if wsclean can find lofar during build time it will be build with the lofar beam. This is useful for lofar people, but may result in a runtime dependency on lofar? need to check

Add dysco

The dysco library adds useful compression capabilities. It can be found in: https://github.com/aroffringa/dysco

KERN-2 LOFAR install - lofarinit.sh

On our systems we've had some issues upgrading to lofar 2.20 from 2.19 (which we installed via kern-dev at the time a few months ago).

I've since attempted to install it myself on a fresh VM Ubuntu install and ran into the same issue - namely when lofar is installed usually there is a lofarinit.sh generated in the root location to source, in this case /usr, which appeared when we installed it before. With this release this fails to appear. I have other issues but I think not initialising correctly might be the cause.

In this case I simply followed the quick steps:

$ sudo apt-get install software-properties-common
$ sudo add-apt-repository -s ppa:kernsuite/kern-2
$ sudo apt-add-repository multiverse
$ sudo apt-get update

And then installed lofar $ sudo apt-get install lofar.

I noticed in the KERN-2 release notes it says:

Split of LOFAR package in smaller packages

So it could be possible that I'm simply missing something. Though what does the above mean practically when attempting to install lofar software?

The other issues include for example not being able to run pybdsm:

adam@adam-VirtualBox:~$ pybdsm
/usr/bin/python: can't open file '/usr/lib/python2.7/site-packages/lofar/bdsm/pybdsm.py': [Errno 2] No such file or directory

update to casacore 2.2.0

kvis complains of no base directory

oms@jake:~$ kvis
Environment variable KARMABASE not found
Error statting "/usr/local/karma" (compiled in)	No such file or directory
Error statting "/usr/local/karma" (default)	No such file or directory
No Karma base directory found!
Port allocated: 12115

I'm not sure if this is just an ignorable warning, or if functionality is affected. @twillis449, could you check please?

Could you package stimela for me

https://github.com/SpheMakh/Stimela

Tables used by the python-casacore measures seem to be missing from pip install

Xenial 16.04 install
Installed kern casacore-dev with apt install
Installed python-casacore in a virtualenv using pip install
Ran montblanc test case which makes use of pyrap.measures
Complaints about missing tables crop up, one producing a SEVERE log message.

(mb) sperkins@simon-Y700:~/work/ska/code/montblanc/montblanc/tests$ python test_cmp_vis.py
test_cmp_visibilities (__main__.TestCmpVis)
Test visibilities produced by montblanc and meqtrees ... 2016-07-18 16:16:05    WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)  Requested data table IERSeop97 cannot be found in the searched directories:
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)+ /usr/share/casacore/data/ephemerides/
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)+ /usr/share/casacore/data/geodetic/
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)  Requested data table IERSpredict cannot be found in the searched directories:
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)+ /usr/share/casacore/data/ephemerides/
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)+ /usr/share/casacore/data/geodetic/
2016-07-18 16:16:05 INFO    MeasIERS::fillMeas(MeasIERS::Files, Double)     Requested JD 51583 is outside the range of the IERS (Earth axis data) table.
2016-07-18 16:16:05 INFO    MeasIERS::fillMeas(MeasIERS::Files, Double) +   Calculations will proceed with less precision
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)  Requested data table TAI_UTC cannot be found in the searched directories:
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)+ /usr/share/casacore/data/ephemerides/
2016-07-18 16:16:05 WARN    MeasIERS::findTab (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasIERS.cc, line 381)+ /usr/share/casacore/data/geodetic/
2016-07-18 16:16:05 SEVERE  MeasTable::dUTC(Double) (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasTable.cc, line 4383)  Cannot read leap second table TAI_UTC
ERROR

======================================================================
ERROR: test_cmp_visibilities (__main__.TestCmpVis)
Test visibilities produced by montblanc and meqtrees
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_cmp_vis.py", line 365, in test_cmp_visibilities
    vis_output=Options.VISIBILITY_OUTPUT_RESIDUALS)
  File "test_cmp_vis.py", line 282, in get_v4_output
    with montblanc.rime_solver(slvr_cfg) as slvr:
  File "/home/sperkins/work/ska/code/montblanc/montblanc/__init__.py", line 148, in rime_solver
    return montblanc.factory.rime_solver(slvr_cfg)
  File "/home/sperkins/work/ska/code/montblanc/montblanc/factory.py", line 175, in rime_solver
    return create_rime_solver_from_ms(RimeSolver, slvr_cfg)
  File "/home/sperkins/work/ska/code/montblanc/montblanc/factory.py", line 147, in create_rime_solver_from_ms
    loader.load(slvr, slvr_cfg)
  File "/home/sperkins/work/ska/code/montblanc/montblanc/impl/rime/v4/loaders/loaders.py", line 126, in load
    parallactic_angles = mbu.parallactic_angles(phase_dir, ref_ant_position, times)
  File "/home/sperkins/work/ska/code/montblanc/montblanc/util/__init__.py", line 459, in parallactic_angles
    pm.posangle(field_centre, zenith).get_value("deg") for t in times])
  File "/home/sperkins/venv/mb/local/lib/python2.7/site-packages/casacore/measures/__init__.py", line 933, in posangle
    return _measures.posangle(self, m0, m1)
RuntimeError: 2016-07-18 16:16:05   SEVERE  MeasTable::dUTC(Double) (file /build/casacore-QQbZwk/casacore-2.1.0/measures/Measures/MeasTable.cc, line 4383)  Cannot read leap second table TAI_UTC

----------------------------------------------------------------------
Ran 1 test in 0.136s

FAILED (errors=1)
(mb) sperkins@simon-Y700:~/work/ska/code/montblanc/montblanc/tests$

wsclean/casacore deps clusterfuck

So I have a 16.04 system. Got this installed:

oms@ike:~/projects/IH-VLA/14A-012/MACSJ0416-S$ dpkg -la|grep casa
ii  casacore-data                        20160711-1kern1                          all          Casacore data files
ii  casarest                             1.4.1-1kern3                             amd64        standalone radio interferometric imager derived from CASA
ii  libcasa-casa2:amd64                  2.1.0-1kern2                             amd64        CASA core modules
ii  libcasa-coordinates2:amd64           2.1.0-1kern2                             amd64        CASA coordinates library
ii  libcasa-fits2:amd64                  2.1.0-1kern2                             amd64        CASA FITS library
ii  libcasa-images2:amd64                2.1.0-1kern2                             amd64        CASA image processing library
ii  libcasa-lattices2:amd64              2.1.0-1kern2                             amd64        CASA lattice library
ii  libcasa-measures2:amd64              2.1.0-1kern2                             amd64        CASA measures library
ii  libcasa-mirlib2:amd64                2.1.0-1kern2                             amd64        CASA mirlib library
ii  libcasa-ms2:amd64                    2.1.0-1kern2                             amd64        CASA MeasurementSet library
ii  libcasa-python2:amd64                2.1.0-1kern2                             amd64        CASA Python bindings
ii  libcasa-scimath-f2:amd64             2.1.0-1kern2                             amd64        CASA scimath F library
ii  libcasa-scimath2:amd64               2.1.0-1kern2                             amd64        CASA basic mathematical modules
ii  libcasa-tables2:amd64                2.1.0-1kern2                             amd64        CASA table system
ii  python-casacore                      2.1.2-1kern2                             amd64        python wrapper for casacore
$

Now I want to install wsclean:

$ sudo apt-get install wsclean
[sudo] password for oms: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  linux-headers-4.4.0-53 linux-headers-4.4.0-53-generic linux-headers-4.4.0-57 linux-headers-4.4.0-57-generic
  linux-image-4.4.0-53-generic linux-image-4.4.0-57-generic linux-image-extra-4.4.0-53-generic linux-image-extra-4.4.0-57-generic
  linux-signed-image-4.4.0-53-generic linux-signed-image-4.4.0-57-generic
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  libboost-date-time1.58.0 libcommon libelementresponse libgsl2 liblog4cplus-1.1-9 libstationresponse libwsclean0
Suggested packages:
...

Running wsclean gives an error (NB: if you just run it without parameters it's ok, it prints the help text. It's actually getting it to open an MS that forces the error.)

$ wsclean foo.ms
wsclean: symbol lookup error: /usr/lib/x86_64-linux-gnu/libwsclean.so.0: undefined symbol: _ZN4casa7QuantumIdEC1Ev

Next, I install casacore-dev to make wsclean work:

$ sudo apt-get install casacore-dev
[sudo] password for oms: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  linux-headers-4.4.0-53 linux-headers-4.4.0-53-generic linux-headers-4.4.0-57 linux-headers-4.4.0-57-generic
  linux-image-4.4.0-53-generic linux-image-4.4.0-57-generic linux-image-extra-4.4.0-53-generic linux-image-extra-4.4.0-57-generic
  linux-signed-image-4.4.0-53-generic linux-signed-image-4.4.0-57-generic
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  libcasa-casa2 libcasa-coordinates2 libcasa-derivedmscal2 libcasa-fits2 libcasa-images2 libcasa-lattices2 libcasa-meas2
  libcasa-measures2 libcasa-mirlib2 libcasa-ms2 libcasa-msfits2 libcasa-python2 libcasa-scimath-f2 libcasa-scimath2 libcasa-tables2
The following NEW packages will be installed:
  casacore-dev libcasa-derivedmscal2 libcasa-meas2 libcasa-msfits2
The following packages will be upgraded:
  libcasa-casa2 libcasa-coordinates2 libcasa-fits2 libcasa-images2 libcasa-lattices2 libcasa-measures2 libcasa-mirlib2 libcasa-ms2
  libcasa-python2 libcasa-scimath-f2 libcasa-scimath2 libcasa-tables2

But now pyrap-measures is broken:

$ python -c "import pyrap.measures"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python2.7/dist-packages/pyrap/measures.py", line 1, in <module>
    from casacore.measures import *
  File "/usr/lib/python2.7/dist-packages/casacore/measures/__init__.py", line 30, in <module>
    import casacore.quanta as dq
  File "/usr/lib/python2.7/dist-packages/casacore/quanta/__init__.py", line 1, in <module>
    from .quantity import quantity, is_quantity
  File "/usr/lib/python2.7/dist-packages/casacore/quanta/quantity.py", line 2, in <module>
    from ._quanta import Quantity
ImportError: /usr/lib/python2.7/dist-packages/casacore/quanta/_quanta.x86_64-linux-gnu.so: undefined symbol: _ZN4casa16throwArrayShapesEPKc

Upgrading python-casacore solves it:

oms@ike:~/projects/IH-VLA/14A-012$ sudo apt-get install python-casacore
Reading package lists... Done  dependencies not installed?
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  linux-headers-4.4.0-53 linux-headers-4.4.0-53-generic linux-headers-4.4.0-57 linux-headers-4.4.0-57-generic
  linux-image-4.4.0-53-generic linux-image-4.4.0-57-generic linux-image-extra-4.4.0-53-generic linux-image-extra-4.4.0-57-generic
  linux-signed-image-4.4.0-53-generic linux-signed-image-4.4.0-57-generic
Use 'sudo apt autoremove' to remove them.
The following packages will be upgraded:
  python-casacore

But now casacore-data is also required, but it hasn't been installed. Once I install that, I finally have a working system (I think....)

SigPyProc package

It would be great to have it.

Installation guide
http://www3.mpifr-bonn.mpg.de/staff/ebarr/sigpyproc/Installation.html

Cheers

update to casa 4.7.1

Could you package GalSim

https://github.com/GalSim-developers/GalSim

Tigger 1.3.4 fails when creating a sky model in kern-dev but not in radio-astro

On kernsuite/kern-dev, tigger-convert (and tigger) fall over on this sky_model.txt. The tigger version is 1.3.4.

$ tigger-convert -f sky_model.txt sky_model.lsm.html
Reading sky_model.txt (ASCII table)
Error loading model: Header update sequence item #0 is invalid; the item must either be a 2-tuple containing a keyword and value, or a 3-tuple containing a keyword, value, and comment string.

However the exact same sky model succeeds on radio-astro/main version of tigger 1.3.4.

Could this be a python 3 issue?

add python-qt4 python-sip dependencies to lofar package

these are required for some of the python scripts.

LD_LIBRARY_PATH and pyrap

I ran into an issue with pyrap while trying to run prefactor (specifically Initial-Subtract-Fast) on top of a Kernsuite installation of LOFAR tools. See prefactor issue #134 for the full thread. The relevant error is below. As discussed at length in the prefactor issue #134 thread, I tried manually setting LD_LIBRARY_PATH to no avail. The problem doesn't appear to be with a corrupted MS either.

In [1]: import pyrap.tables as pt

In [2]: my_ms = '/data/t1data/hba/results_L523928_calpost/L523928_SB000_uv.dppp_1287E19ABt_159MHz.pre-cal.ms/'

In [3]: pt.addDerivedMSCal(my_ms)
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-3-d266bf2f8376> in <module>()
----> 1 pt.addDerivedMSCal(my_ms)

/usr/lib/python2.7/dist-packages/casacore/tables/msutil.pyc in addDerivedMSCal(msname)
    170     # Add all columns using DerivedMSCal as data manager.
    171     dminfo = {"TYPE": "DerivedMSCal", "NAME": "", "SPEC": {}}
--> 172     t.addcols (maketabdesc(descs), dminfo)
    173     # Flush the table to make sure it is written.
    174     t.flush()

/usr/lib/python2.7/dist-packages/casacore/tables/table.pyc in addcols(self, desc, dminfo, addtoparent)
   1137                 cd = casacore.tables.tableutil.makecoldesc (desc['name'], desc)
   1138                 tdesc = casacore.tables.tableutil.maketabdesc(cd)
-> 1139         self._addcols (tdesc, dminfo, addtoparent)
   1140         self._makerow()
   1141 

RuntimeError: Table DataManager error: Data Manager class  is not registered
  Check (DY)LD_LIBRARY_PATH matches the libraries used during the build of

In [5]: tab = pt.table(my_ms, ack=False)

In [6]: global_el_values = tab.getcol('AZEL1', rowincr=10000)[:, 1]
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-6-ffd03a496cfd> in <module>()
----> 1 global_el_values = tab.getcol('AZEL1', rowincr=10000)[:, 1]

/usr/lib/python2.7/dist-packages/casacore/tables/table.pyc in getcol(self, columnname, startrow, nrow, rowincr)
    949 #                i = inx*
    950 #        except:
--> 951         return self._getcol (columnname, startrow, nrow, rowincr)
    952 
    953     def getcolnp (self, columnname, nparray, startrow=0, nrow=-1, rowincr=1):

RuntimeError: TableProxy::getColumn: column AZEL1 does not exist

In [7]: tab.close()

In [8]: pt.removeDerivedMSCal(my_ms)

In [9]:

aoflagger/lofar NDPPP shared library missing

NDPPP is complaining about a missing shared library for aoflagger (libdppp.aoflag.so). I've uninstalled and reinstalled both lofar and aoflagger to no avail.

Example error:

terminate called after throwing an instance of 'casa::AipsError' what(): Shared library aoflag not found in CASACORE_LDPATH or (DY)LD_LIBRARY_PATH libdppp_aoflag.so: cannot open shared object file: No such file or directory

python-tigger install fails on missing libicu52 dependency

Xenial 16.04 system
Add kernsuite PPA
bash $ sudo apt-get install software-properties-common $ sudo add-apt-repository -s ppa:kernsuite/kern-dev
Installed meqtrees-timba, python-meqtrees-cattery, python-owlcat
Fell over on the following command

$ sudo apt install python-tigger
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 python-tigger : Depends: libicu52 but it is not installable
E: Unable to correct problems, you have held broken packages.

package up heasoft

x-ray people will be happy

http://heasarc.nasa.gov/lheasoft/