It seemed I had everything but flex. I downloaded that and double-checked all of the dependencies. Everything compiles now but I'm getting a linking error.

I am using a CLEAN install of cygwin with the following packages:

setup -P cygwin,autoconf,automake,binutils,bison,bzip2,cygport,diffutils,fileutils,findutils,flex,gawk,gcc,git,libtool,make,patch,pkg-config,sed,tar,w32api,dri-drivers,libbz2_1,libfontenc1,libfreetype6,libgcc1,libGL1,libpixman1_0,libX11_6,libXau6,libXdmcp6,libXext6,xauth,xcursor-themes,xkbcomp,xkeyboard-config,zlib0,libdmx1,libXaw7,libXfixes3,libXi6,libXmu6,libXmuu1,libXrender1,libXt6,bigreqsproto,compositeproto,damageproto,dmxproto,fixesproto,font-util,fontsproto,glproto,inputproto,kbproto,libXfont-devel,randrproto,recordproto,renderproto,resourceproto,scrnsaverproto,windowswmproto,xcmiscproto,xextproto,xf86bigfontproto,xineramaproto,xorg-util-macros,xproto,xtrans,khronos-opengl-registry,libpixman1-devel,libx11-devel,libgl-devel,libxkbfile-devel,libxcb-image-devel,lib-icccm-devel,glapi-devel

Prepping, generating, and configuring:

cygport xorg-server.cygport prep
autogen.sh -V
configure

And on make I get the attached linker error. I've tried cleaning and redownloading twice now.

> I think now might be an appropriate time to ask if you have all the
> prerequisites listed in [1]?

Yes, I do. On that note, the prerequisites are missing:

libpixman1-devel
libx11-devel
libgl-devel
libxkbfile-devel
libxcb-image-devel
lib-icccm-devel

(detected during configure)

and

glapi-devel

(detected at compile-time)

There is also no sanity check for flex, although it is listed as a prerequisite.

/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: warning: 
cannot find entry symbol rrwarn=E_BAD_PTR_
INT_COMBINATION; defaulting to 00401000
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function 
`glxWinScreenSwapInterval':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:467:
 undefined reference to `_wglSwapIn
tervalEXTWrapper'
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function 
`glxWinDrawableDestroy':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:932:
 undefined reference to `_wglDestro
yPbufferARBWrapper'
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function `glxWinReleaseDC':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:1242:
 undefined reference to `_wglRelea
sePbufferDCARBWrapper'
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function 
`glxWinCreateContext':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:1624:
 undefined reference to `_glWinSet
upDispatchTable'
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function 
`fbConfigToPixelFormatIndex':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:1803:
 undefined reference to `_wglChoos
ePixelFormatARBWrapper'
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function `glxWinMakeDC':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:1204:
 undefined reference to `_wglGetPb
ufferDCARBWrapper'
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function 
`glxWinContextMakeCurrent':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:1497:
 undefined reference to `_wglMakeC
ontextCurrentARBWrapper'
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:1328:
 undefined reference to `_wglCreat
ePbufferARBWrapper'
../../hw/xwin/glx/.libs/libXwinGLX.a(indirect.o): In function 
`glxWinScreenProbe':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:596:
 undefined reference to `_wglResolv
eExtensionProcs'
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:603:
 undefined reference to `_wglGetExt
ensionsStringARBWrapper'
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:2087:
 undefined reference to `_wglGetPi
xelFormatAttribivARBWrapper'
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/hw/xwin/glx/indirect.c:2171:
 undefined reference to `_wglGetPi
xelFormatAttribivARBWrapper'
../../glx/.libs/libglx.a(glxcmds.o): In function `FlushContext':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/glx/dispatch.h:5827: 
undefined reference to `__glapi_tls_Dispa
tch'
../../glx/.libs/libglx.a(glxcmds.o): In function `DoMakeCurrent':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/glx/dispatch.h:5827: 
undefined reference to `__glapi_tls_Dispa
tch'
../../glx/.libs/libglx.a(glxcmds.o): In function `__glXDisp_WaitGL':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/glx/dispatch.h:5811: 
undefined reference to `__glapi_tls_Dispa
tch'
../../glx/.libs/libglx.a(glxcmds.o): In function `__glXDisp_CopyContext':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/glx/dispatch.h:5811: 
undefined reference to `__glapi_tls_Dispa
tch'
../../glx/.libs/libglx.a(glxcmds.o): In function `__glXDisp_SwapBuffers':
/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/glx/dispatch.h:5811: 
undefined reference to `__glapi_tls_Dispa
tch'
../../glx/.libs/libglx.a(glxcmds.o):/usr/src/xorg-server-1.14.1-1/src/xserver-cygwin-1.14.1-1/glx/dispatch.h:5811:
 more
undefined references to `__glapi_tls_Dispatch' follow
collect2: ld returned 1 exit status
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