I was developing a website that had common logic held in a portable class library. However when I used Git deployment, the compilation on the Azure servers would fail with:
The reference assemblies for framework ".NETPortable,Version=v4.5,Profile=Profile78" were not found.

After much debugging it seems the issue is that the Azure build servers don’t have all the PCL profiles. As a shot term fix, you can go into your PCL properties, and remove support for Windows Phone 8. I changed my project to only support Windows 4.5 & Windows store, and this resolved the issue.