Let's fix that logic to be case insensitive on the file extension.
Yishai responded in email:
I changed the mzID to mzid and now it says there are no spectra. Also tried changing mzML to mzml.
System.IO.IOException: ERROR: No spectra were found for the new library.
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& ambiguous) in C:\proj\skyline_4_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 171
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 137
Are the .mzid and .mzML (usually capitalized like this) in the same directory? It may be that the library builder is having trouble finding the mzML, but I would expect it to give an error about not being able to find a file rather than not having any spectra.
Matt may still need to get your files, which you can upload to: