Try #1058:

src/backwards_compatible_isolation.jl

@@ -484,9 +484,10 @@ function with_dependencies_loadable_at_toplevel(f, mainctx::Context, pkg::Packag
         empty!(localctx.env.project.deps)
         localctx.env.project.deps[pkg.name] = pkg.uuid
         seen_uuids = Set{UUID}()
-        # Only put `pkg` and its deps (recursively) in the temp project
-        collect_deps!(seen_uuids, pkg)
     end
+    # Only put `pkg` and its deps (recursively) in the temp project
+    seen_uuids = Set{UUID}()
+    collect_deps!(seen_uuids, pkg)
 
     pkgs = PackageSpec[]
     if target !== nothing

test/pkg.jl

@@ -688,6 +688,15 @@ end
     end end
 end
 
+@testset "building project should fix version of deps" begin
+    temp_pkg_dir() do project_path
+        dep_pkg = joinpath(@__DIR__, "test_packages", "BuildProjectFixedDeps")
+        Pkg.activate(dep_pkg)
+        Pkg.build()
+        @test isfile(joinpath(dep_pkg, "deps", "artifact"))
+    end
+end
+
 include("repl.jl")
 include("api.jl")
 include("registry.jl")

test/test_packages/BuildProjectFixedDeps/.gitignore

@@ -0,0 +1,2 @@
+deps/artifact
+deps/build.log

test/test_packages/BuildProjectFixedDeps/Manifest.toml

@@ -0,0 +1,92 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[BenchmarkTools]]
+deps = ["JSON", "Printf", "Statistics", "Test"]
+git-tree-sha1 = "5d1dd8577643ba9014574cd40d9c028cd5e4b85a"
+uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+version = "0.4.2"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[JSON]]
+deps = ["Dates", "Distributed", "Mmap", "Sockets", "Test", "Unicode"]
+git-tree-sha1 = "fec8e4d433072731466d37ed0061b3ba7f70eeb9"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.19.0"
+
+[[LibGit2]]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

test/test_packages/BuildProjectFixedDeps/Project.toml

@@ -0,0 +1,7 @@
+name = "BuildProjectFixedDeps"
+uuid = "a9d53770-2f9b-11e9-234d-75f2cd7ebf28"
+version = "0.1.0"
+
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

test/test_packages/BuildProjectFixedDeps/deps/build.jl

@@ -0,0 +1,5 @@
+import Pkg
+build_artifact = joinpath(@__DIR__, "artifact")
+isfile(build_artifact) && rm(build_artifact)
+@assert Pkg.installed()["JSON"] == v"0.19.0"
+touch(build_artifact)

test/test_packages/BuildProjectFixedDeps/src/BuildProjectFixedDeps.jl

@@ -0,0 +1,5 @@
+module BuildProjectFixedDeps
+
+greet() = print("Hello World!")
+
+end # module