Hi all, I'm working to install bisque from source, and I'm running into a couple errors walking through the tutorial here
I'm going to try to log all the different errors I'm getting here, but I think the significant one regards imgcnv, and it is the last part highlighted below.
My errors begin running bisque-bootstrap.py:
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from mahotas/numpypp/array.hpp:17:0,
from mahotas/_histogram.cpp:10:
mahotas/numpypp/numpy.hpp:11:33: fatal error: numpy/ndarrayobject.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Failed building wheel for mahotas
Running setup.py clean for mahotas
Failed to build mahotas
So, I activate bqenv and run pip install -r requirements.txt, but everything, including mahotas, appears to be satisfied, so I continue.
paver setup server appears to run without issues.
Running bq-admin setup, I use all the default variables unless otherwise noted. Choosing to deploy all static resources to public directory leads to errors. I'm not entirely sure what this option means, but I'm doing this as an exercise and not planning on deploying any public servers any time soon, so I continue on.
I choose N to Change a site variable?
N to enable mail delivery.
After choosing to initialize the new database,
15:11:51,741 ERROR [bq.websetup] Issue loading ingest_service = bq.ingest.controllers.ingest_server
Traceback (most recent call last):
File "/home/austin/bisque/bqcore/bq/websetup/schema.py", line 23, in setup_schema
service = x.load()
File "/home/austin/bisque/bqenv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line
2332, in load
return self.resolve()
File "/home/austin/bisque/bqenv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line
2338, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/home/austin/bisque/bqserver/bq/ingest/controllers/ingest_server.py", line 19, in <module>
from bq import image_service
File "/home/austin/bisque/bqserver/bq/image_service/__init__.py", line 2, in <module>
from api import *
File "/home/austin/bisque/bqserver/bq/image_service/api.py", line 62, in <module>
from controllers.service import ImageServiceController as LocalImageServer
File "/home/austin/bisque/bqserver/bq/image_service/controllers/service.py", line 32, in <module>
from .imgsrv import ImageServer, getOperations
File "/home/austin/bisque/bqserver/bq/image_service/controllers/imgsrv.py", line 51, in <module>
from .converters.converter_imgcnv import ConverterImgcnv
File "/home/austin/bisque/bqserver/bq/image_service/controllers/converters/converter_imgcnv.py", l$
ne 53, in <module>
imgcnvlib = ctypes.cdll.LoadLibrary(imgcnv_lib_name)
File "/usr/lib/python2.7/ctypes/__init__.py", line 440, in LoadLibrary
return self._dlltype(name)
File "/usr/lib/python2.7/ctypes/__init__.py", line 362, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libimgcnv.so: cannot open shared object file: No such file or directory
then four similar errors with the same root issue. I run bq-admin server start anyways, and unsurprisingly I see a nearly page with title "Server Error" and the uninformative line "An Unexpected exception:"
I stop the server.
I take the following action:
(bqenv) austin@karlsplatz:~/bisque$ apt list | grep libimgcnv
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
libimgcnv/unstable 2.2.2-1 amd64
As I read on in the tutorial, I see mention of imgcnv, but I am running on Ubuntu 16.04, so I would assume that
following these instructions (https://biodev.ece.ucsb.edu/projects/bisquik/wiki/CbiDebian) should work. However, I ran those lines previously and am still having this issue, so I try again, and here's some potentially relevant output from apt-get update
AppStream cache update completed, but some metadata was ignored due to errors.
Reading package lists... Done
Output from install attempts:
(bqenv) austin@karlsplatz:~/bisque$ sudo apt-get install imgcnv libimgcnv
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:
imgcnv : Depends: libavcodec56 (>= 10:2.6.9) but it is not installable
Depends: libavformat56 (>= 10:2.6.9) but it is not installable
Depends: libavutil54 (>= 10:2.6.9) but it is not installable
Depends: libgdcm2.4 but it is not installable
Depends: libswresample1 (>= 10:2.6.9) but it is not installable
Depends: libswscale3 (>= 10:2.6.9) but it is not installable
libimgcnv : Depends: libavcodec56 (>= 10:2.6.9) but it is not installable
Depends: libavformat56 (>= 10:2.6.9) but it is not installable
Depends: libavutil54 (>= 10:2.6.9) but it is not installable
Depends: libgdcm2.4 but it is not installable
Depends: libswresample1 (>= 10:2.6.9) but it is not installable
Depends: libswscale3 (>= 10:2.6.9) but it is not installable
E: Unable to correct problems, you have held broken packages.
The other two packages (libopenjpeg5 and libopenslide-dev) appear to install without issue.
Ultimately, it seems like there is an issue with imgcnv, and maybe there are other issues at work here too. I include all this detail in case there's something (like an option in setup) that I am choosing incorrectly.