Can make manually but not via PKGBUILD

I'm trying to install exonerate from the AUR, where it is now an orphan. When I run makepkg -s, it fails.
The PKGBUILD looked a little bit funny (just old?) so I attempted to expand and modify the build section as follows.
build() {
cd "$pkgname-$pkgver"
./configure --prefix=/usr
make
check() {
cd "$pkgname-$pkgver"
make check
package() {
cd "$pkgname-$pkgver"
make DESTDIR="$pkgdir/" install
This did not help.
Further, if I download the upstream source files I can run `./configure` then `make` fine, which seeemed to imply to me that the BUILDPKG should work fine. Is there a way to install this via pacman?

Salkay wrote:
Scimmia wrote:1. You could, but it's kind of heavy handed. You should mess with the variables and see exactly what's causing the problem. You can then modify the variables before running make.
I'm having a bit of trouble finding exactly how to do this. Would you have a reference that I could read?
Also, you say "heavy handed", but if this builds okay, would the resulting compiled file be essentially the same as the files if I tweaked the variables more precisely? What advantage would there be in defining variables more precisely?
I don't have a reference. You can do it by changing the variables in makepkg.conf, but what I would do is to leave !buildflags in the options, then copy the variable definitions into the build function in the PKGBUILD. The defaults would look like this:
export CPPFLAGS="-D_FORTIFY_SOURCE=2"
export CFLAGS="-march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4"
export CXXFLAGS="-march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4"
export LDFLAGS="-Wl,-O1,--sort-common,--as-needed,-z,relro"
That should fail to build. You can then comment out each of them to see which one is causing the failure. Once you know that, you can remove the flags one at a time to figure out exactly which one is causing the failure.
As to what they do, you can check the gcc documentation. Google each of the flags and it should point you to the right part.

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