'ghc-pkg update' fails due to bad file descriptor error

In the final part of installation when packages are registered, the following command fails

"inplace/bin/ghc-cabal" register libraries/ghc-prim dist-install "/home/pgrads/mp16005/linux/installed-ghc/lib/ghc-8.2.0.20170708/bin/ghc" "/home/pgrads/mp16005/linux/installed-ghc/lib/ghc-8.2.0.20170708/bin/ghc-pkg" "/home/pgrads/mp16005/linux/installed-ghc/lib/ghc-8.2.0.20170708" '' '/home/pgrads/mp16005/linux/installed-ghc' '/home/pgrads/mp16005/linux/installed-ghc/lib/ghc-8.2.0.20170708' '/home/pgrads/mp16005/linux/installed-ghc/share/doc/ghc-8.2.0.20170708/html/libraries' NO

with the following output

Registering library for ghc-prim-0.5.0.0..
ghc-cabal:
'/home/pgrads/mp16005/linux/installed-ghc/lib/ghc-8.2.0.20170708/bin/ghc-pkg'
exited with an error:
ghc-pkg: Couldn't open database
/home/pgrads/mp16005/linux/installed-ghc/lib/ghc-8.2.0.20170708/package.conf.d
for modification: {handle:
/home/pgrads/mp16005/linux/installed-ghc/lib/ghc-8.2.0.20170708/package.conf.d/package.cache.lock}:
hLock: invalid argument (Bad file descriptor)

It might be something to do with the permissions I have on my machine but I used to be able to install ghc if I gave it a suitable prefix other than /usr/local.

A workaround is to make sure that HAVE_FLOCK is not defined, the way I did this was commenting out the three relevant lines in libraries/base/configure.ac.

geekosaur suggests on IRC that the problem might be

what might be possible is that hLock uses fcntl locking, ghc-pkg opens a database r/o if it can't open it r/w, and it tried to acquire a write lock (which will fail with EBADF if the file descriptor is only open for read). and there is an SElinux context prohibiting your process opening the db for write