It means, that the “manifest.toml” of the project is not valid.
I had this warning, when i tried to create a sysimage without any package.
So my personal default is:
using Pkg
cd(Base.source_dir())
Pkg.activate(".")
Pkg.update()
"StatsPlots" ∉ keys(Pkg.project().dependencies) && Pkg.add("StatsPlots")
The installation of “StatsPlots” (or another package) creates a valid “manifest.toml”
for the PackageCompiler and the compiler can generate a sysimage without warning.