Reinstall vs svn update?

Hi folks,

Quick question: are there significant differences between versions r11100 and HEAD as of this morning (11413) which would require a re-compiling of some underlying libraries, or will a simple svn update -r HEAD & make be sufficient? We’re experiencing the same problem as http://forum.image.sc/t/opening-flex-files/18513/7&hilit=flex#p5342, and wanted to update rather than roll back.

Thanks,

Lee.

I think you’ll have to run:

python CellProfiler.py --build-and-exit

to recompile the Cython files. We’re relying more heavily on the h5py package now. Previously, it was needed to run Ilastik, now it’s needed for general CellProfiler usage. If you don’t have this installed, there are nice Windows installers at http://www.lfd.uci.edu/~gohlke/pythonlibs/ for 32 and 64-bit Python. We’ve had some difficulties with h5py for the Mac, but the documentation for installing it can be found at http://www.cellprofiler.org/wiki/index.php/Building_CellProfiler2.0.app_on_a_Mac#HDF5_and_h5py .

For Linux, the best resource is the build script, “Makefile.CP2”, which can be found in SVN.

–Lee

Hi Lee,

When I run this, everything seems fine. However, when I try then to load a pipeline (any pipeline), I get a crash. I’ll cross post to the CellProfiler2 Bugs forum, but I think there’s a bug in CP2 (or in the WX install) for the version I have (svn r 11418). Do you know of a stable version where the FLEX file bug introduced between 10*** and 11010 has been fixed?

Here’s some debugging output from the terminal

code: Gtk-CRITICAL : gtk_range_set_range: assertion `min < max’ failed
INFO:root:Subversion revision: 11418
Subversion revision: 11418
ERROR:cellprofiler.gui.moduleview:WX internal error detected
Traceback (most recent call last):
File “/usr/cp2/CellProfiler/cellprofiler/gui/moduleview.py”, line 1732, in CalcMin
if self.get_item(col,j) is not None])
File “/usr/cp2/CellProfiler/cellprofiler/gui/moduleview.py”, line 1688, in get_item
return self.__items[j]

IndexError: list index out of range
WX internal error detected
Traceback (most recent call last):
File “/usr/cp2/CellProfiler/cellprofiler/gui/moduleview.py”, line 1732, in CalcMin
if self.get_item(col,j) is not None])
File “/usr/cp2/CellProfiler/cellprofiler/gui/moduleview.py”, line 1688, in get_item
return self.__items[j]

IndexError: list index out of range

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x00007fba18c01756, pid=23325, tid=140437446690560

JRE version: 6.0_20-b20

Java VM: OpenJDK 64-Bit Server VM (19.0-b09 mixed mode linux-amd64 compressed oops)

Derivative: IcedTea6 1.9.8

Distribution: Red Hat Enterprise Linux Server release 6.1 (Santiago), package rhel-1.39.1.9.8.el6_1-x86_64

Problematic frame:

C [core.so+0x70756] _ZN9wxPySizer7CalcMinEv+0xc6

[/code]

[quote=“LeeKamentsky”]I think you’ll have to run:

python CellProfiler.py --build-and-exit

to recompile the Cython files. We’re relying more heavily on the h5py package now. Previously, it was needed to run Ilastik, now it’s needed for general CellProfiler usage. If you don’t have this installed, there are nice Windows installers at http://www.lfd.uci.edu/~gohlke/pythonlibs/[/quote]

For Linux, the best resource is the build script, “Makefile.CP2”, which can be found in SVN.

–Lee*