I've got similar issue as described in #536 but for node.js v0.12.3, when building v0.4.0 on Windows.

$ npm install nodegit@0.4.0
\

nodegit@0.4.0 install c:\Projects\gitws\BOF\node_modules\nodegit
node lifecycleScripts/install

[nodegit] Fetching binary from S3.
[nodegit] Failed to install prebuilt binary, building manually.
[nodegit] Making sure dependencies are available and native code is generated
[nodegit] Everything is ready to go, attempting compilation
[nodegit] Building native node module.
{ [Error: Command failed: C:\WINDOWS\system32\cmd.exe /s /c "c:\Projects\gitws\BOF\node_modules\nodegit\node_modules.bi
n\pangyp rebuild"
gyp ERR! build error
gyp ERR! stack Error: C:\Program Files (x86)\MSBuild\12.0\bin\msbuild.exe failed with exit code: 1
gyp ERR! stack at ChildProcess.onExit (c:\Projects\gitws\BOF\node_modules\nodegit\node_modules\pangyp\lib\build.js:2
71:23)
gyp ERR! stack at ChildProcess.emit (events.js:110:17)
gyp ERR! stack at Process.ChildProcess._handle.onexit (child_process.js:1074:12)
gyp ERR! System Windows_NT 6.1.7601
gyp ERR! command "node" "c:\Projects\gitws\BOF\node_modules\nodegit\node_modules\pangyp\bin\node-gyp.js" "rebui
ld"
gyp ERR! cwd c:\Projects\gitws\BOF\node_modules\nodegit
gyp ERR! node -v v0.12.3
gyp ERR! pangyp -v v2.2.0
gyp ERR! not ok
]
killed: false,
code: 1,
signal: null,
cmd: 'C:\WINDOWS\system32\cmd.exe /s /c "c:\Projects\gitws\BOF\node_modules\nodegit\node_modules.bin\pangy
p rebuild"' }
undefined

nodegit@0.4.0 postinstall c:\Projects\gitws\BOF\node_modules\nodegit
node lifecycleScripts/clean

[nodegit] Cleaning up after ourselves.
[nodegit] Deleting unneeded files.
[nodegit] Finished deleting files.
[nodegit] Pruning devdependencies.
[nodegit] Cleaning unneeded dependencies.
npm WARN uninstall not installed in c:\Projects\gitws\BOF\node_modules\nodegit\node_modules: "for-node-webkit"
unbuild fs-extra@0.18.3
unbuild which-native-nodish@1.1.1
unbuild node-pre-gyp@0.6.7
unbuild npm@2.10.0
[nodegit] Successfully cleaned unneeded dependencies.
unbuild lodash@3.8.0
unbuild combyne@0.8.0
unbuild nan@1.7.0
unbuild request@2.55.0
unbuild js-beautify@1.5.5
unbuild mocha@2.2.5
unbuild tar@2.1.1
unbuild istanbul@0.3.14
unbuild coveralls@2.11.2
unbuild jshint@2.7.0
unbuild pangyp@2.2.0
unbuild nw-gyp@0.12.4
unbuild lcov-result-merger@1.0.2
[nodegit] Failed pruning devdependencies.
[nodegit] Couldn't finish cleaning.
nodegit@0.4.0 node_modules\nodegit
├── promisify-node@0.1.5 (nodegit-promise@1.0.2)
├── which-native-nodish@1.1.1 (find-parent-dir@0.3.0, nodegit-promise@1.0.2)
├── nodegit-promise@2.0.1 (asap@2.0.3)
└── npm@2.10.0