"missing from vendor" even though it is there

What version of `dep` are you using (`dep version`)?

v0.5.4-2-g5600de07

What `dep` command did you run?

Minimally reproducible example:

$ cd $GOPATH/src/github.com/whatever/project
$ ls
main.go
$ cat main.go
package main

import (
    _ "golang.zx2c4.com/wireguard/wgctrl"
)
$ dep init
$ cat Gopkg.toml
[[constraint]]
  branch = "master"
  name = "golang.zx2c4.com/wireguard/wgctrl"

[prune]
  go-tests = true
  unused-packages = true
$ cat Gopkg.lock
[[projects]]
  branch = "master"
  digest = "1:6b3b719432ce543e68c97ebcfc503ba239782ad78e658d363436c7181fdff7a8"
  name = "github.com/mdlayher/genetlink"
  packages = ["."]
  pruneopts = "UT"
  revision = "e35f2bf499b9e396bf88e96af81ac1085f5c6f0b"

[[projects]]
  branch = "master"
  digest = "1:7e464212ab9ff806389ade611ea95503c15900cbc6648191b470575413b73024"
  name = "github.com/mdlayher/netlink"
  packages = [
    ".",
    "nlenc",
  ]
  pruneopts = "UT"
  revision = "4e5dd4017dae8175b908a6bd46b1cb7161664633"

[[projects]]
  branch = "master"
  digest = "1:c79dab329e903f5f7793c3f541645f5e4fdaeb222ccd804b0913ea796d0f0213"
  name = "golang.org/x/crypto"
  packages = ["curve25519"]
  pruneopts = "UT"
  revision = "71b5226ff73902d121cd9dbbdfdb67045a805845"

[[projects]]
  branch = "master"
  digest = "1:1fc1c03687700856ef340d185fd0272e3de88b3a5632283ba3f148cf40c5dcc8"
  name = "golang.org/x/net"
  packages = ["bpf"]
  pruneopts = "UT"
  revision = "a7b16738d86b947dd0fadb08ca2c2342b51958b6"

[[projects]]
  branch = "master"
  digest = "1:ee82b03e3db19a6d3ed88db62427809f5dfc18c3bd1afa30f8c2b7e56c6c7565"
  name = "golang.org/x/sys"
  packages = [
    "unix",
    "windows",
  ]
  pruneopts = "UT"
  revision = "d223b2b6db03988709bac9e66576ad6ec0d83695"

[[projects]]
  digest = "1:66bf404c97d65e646d3c95f76c64dd867d6b0972cf797a06341b3b8dc66d4f65"
  name = "golang.zx2c4.com/wireguard"
  packages = ["ipc/winpipe"]
  pruneopts = "UT"
  revision = "7c97fdb1e34babf2697a815b8381037220e0c19b"
  version = "v0.0.20190908"

[[projects]]
  branch = "master"
  digest = "1:91e8e083d860ea7a5e9d1e506c94d38d487d1c70d4cc78f4fe46182ef4c18d6b"
  name = "golang.zx2c4.com/wireguard/wgctrl"
  packages = [
    ".",
    "internal/wginternal",
    "internal/wglinux",
    "internal/wglinux/internal/wgh",
    "internal/wgopenbsd",
    "internal/wgopenbsd/internal/wgh",
    "internal/wguser",
    "wgtypes",
  ]
  pruneopts = "UT"
  revision = "599d41c32142c0c277590bdfa680795b2b5582a5"

[solve-meta]
  analyzer-name = "dep"
  analyzer-version = 1
  input-imports = ["golang.zx2c4.com/wireguard/wgctrl"]
  solver-name = "gps-cdcl"
  solver-version = 1
$ dep check
# vendor is out of sync:
golang.zx2c4.com/wireguard/wgctrl: missing from vendor
$ stat vendor/golang.zx2c4.com/wireguard/wgctrl/
# It's definitely there

What did you expect to see?

dep check should exit 0, and not complain that it can't find a vendor directory that is in fact present

What did you see instead?

dep check does not exit 0, and complains that it can't find a vendor directory, but is is there

I've been hacking away at this for the last few hours with many different combinations of imports in Gopkg.lock but I can't get dep check to succeed; it always reports a vendor inconsistency problem but the vendored files are definitely there.

The dependency repository is golang.zx2c4.com/wireguard/wgctrl, and I am able to successfully go get golang.zx2c4.com/wireguard/wgctrl.

Any pointers would be appreciated.

golang / dep