Closed gtluu closed 11 months ago
only occurs when using timsconvert backend
Boost interprocess error is most likely caused by use of pynumpress
package in psims
, which is compiled via Cython.
If you can tell me what array_type
is when it's blowing up, I can patch it up.
If you can tell me what
array_type
is when it's blowing up, I can patch it up.
Thanks for the offer, though I believe it's already been fixed in one of your updates last year/earlier this year. I realized I was using the newer array_type
(tuple (array_type, array)
) instead of the older one (tuple (str name, array)
). This has been temporarily fixed.
This is more of a Bruker API issue that requires older versions of psims
(<= 0.1.34) before pynumpress
began being used. I don't know exactly how/why, but pynumpress
doesn't seem to work well with the logger in Bruker's API on Linux. My current thoughts were to fork the current version of psims
and use the older version of psims/mzml/binary_encoding.py that didn't use pynumpress
. Though if there's a better solution I'm all ears.
It'd be simple enough to block the import of pynumpress
via an environment variable.
What's the actual error that the Bruker library generates when pynumpress
is imported?
It's boost::interprocess::interprocess_exception
referenced in issues 8 and 13.
`>>>>>>>>|- ERROR in [bdal-logconf:logger_config.cpp:379] - XML analysis error: The resulting configuration is unusable - Falling back to default configuration: Dynamic exception type: std::bad_cast std::exception::what: std::bad_cast
terminate called after throwing an instance of 'boost::interprocess::interprocess_exception' what(): boost::interprocess::intermodule_singleton initialization failed .command.sh: line 3: 79273 Aborted`
Also, I'm not sure if this helps but this error has also occurred in MSFragger before.
I've added an environment variable PSIMS_NO_PYNUMPRESS
which if it has a non-empty value will skip importing pynumpress
and its features will be disabled in release v0.1.47
.
I've added an environment variable
PSIMS_NO_PYNUMPRESS
which if it has a non-empty value will skip importingpynumpress
and its features will be disabled in releasev0.1.47
.
Thank you for that. Unfortunately, the error still appears without loading pynumpress, so I will need to look into this issue again to see if I've missed something.
This appears to have been fixed as of 62ef7b2e4af17b95fde8f753424cad8dda8fa921 which uses psims 1.2.7.
TIMSCONVERT 1.5.0 was tested on Python 3.11.5 installed with Anaconda 2023.7-2 on Windows 10 22H2 and Ubuntu 22.04.3 LTS.
psims >= 0.1.35 causes Bruker API to throw Boost interprocess error on Linux psims <= 0.1.45? causes the following error when trying to write out ion mobility arrays (this does not occur if
--exclude_mobility
flag is included):File "~/psims/mzml/writer.py", line 549, in spectrum array, encoding=encoding[array_type], compression=compresssion, array_type=array_type, TypeError: unhashable type: dict