[Bioc-devel] mzR will drop mzData file format support

[Neumann, Steffen]

Hi,

some weeks later with mzR-3.9.3 the mzData support has now been
removed, and the embedded proteowizard code updated. This also fixes
the build errors that were present for a while. Thanks for your
patience. If any issues crop up, please use the mzR issue tracker on
github. 

Yours,
Steffen


On Wed, 2021-11-17 at 08:42 +0000, Neumann, Steffen wrote:
> Hi, 
> 
> mzR will soon get the long-awaited update of the embedded
> proteowizard
> [1] as a nice christmas present. Part of that update is the removal
> of
> the older Ramp Backend, which results in dropping the ability to read
> the mass spectrometry file format mzDdata.
> 
> If there is anyone out there who needs mzData for some production
> pipeline, please speak up now. It would be possible to port the old
> mzData support on top the new proteowizard, but we will not be able 
> to do that (I tried, and grew a fair amount of new grey hair). I can
> do
> a bit of hand-holding on the steps that would be required. 
> 
> Conversion of mzData to mzML is possible with the OpenMS
> FileConverter
> tool [2].
> 
> mzR will continue to support mzML, netCDF and mzXML.
> 
> We will accirdingly change mzData files in the msdata package to
> mzML. 
> 
> Yours,
> Steffen
> 
> [1] 
> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsneumann%2FmzR%2Ftree%2Ffeature%2FupdatePwiz_3_0_21263&data=04%7C01%7C%7C1c72cd6d3b8242771c6608d9a9a65e07%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C637727354868819389%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=TUTliMJ4K9NpuGPn9qRu00euwQ%2BIMoS0tphWPskS7g4%3D&reserved=0
> [2] 
> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabibuilder.informatik.uni-tuebingen.de%2Farchive%2Fopenms%2FDocumentation%2Fnightly%2Fhtml%2FTOPP_FileConverter.html&data=04%7C01%7C%7C1c72cd6d3b8242771c6608d9a9a65e07%7C0934ee6c2a574efd80a9fc003defef4e%7C0%7C0%7C637727354868819389%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=SQ0K%2FPruugqSgN3bHMOXl%2BOSORmJgL0d7h385m8sLmU%3D&reserved=0
> 
-- 
---
IPB Halle                    Bioinformatics and Scientific Data
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409