Error building RAxML8 with MacPorts

[mcottrell]

MacPorts? is complaining about the compiler being used to build RAxML8.

I think MacPorts? would rather see the code use simple "cc" rather than be forced to use "gcc". I believe that the Portfile figures out that cc really means clang. That's what happens elsewhere in the build.

I tried to do some patching myself, but I can't patch the RAxML code because it is packed in a compressed file and only later unpacked during the build.

In the error below you will see:

:info:build gcc: Error: You should be using ${configure.cc} :info:build See ​https://trac.macports.org/wiki/UsingTheRightCompiler

Yes, we are already using ${configure.cc} as suggested. The problem is the hard coded gcc, I think.

Here is the error:

:info:build [07:35.N] ------------------------------------------------ Make RAxML8
:info:build make[5]: Entering directory `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/trunk/GDE/RAxML8'
:info:build (DIR=builddir.SSE3.PTHREADS; \
:info:build 	rm -rf $DIR &&\
:info:build 	mkdir $DIR &&\
:info:build 	tar -C $DIR --strip-components=1 -xzf standard-RAxML-8.0.26.tar.gz &&\
:info:build 	arb_sed -i 's/-march=native//' $DIR/Makefile*)
:info:build touch unpack.SSE3.PTHREADS.stamp -r standard-RAxML-8.0.26.tar.gz	
:info:build (DIR=builddir.PTHREADS; \
:info:build 	rm -rf $DIR &&\
:info:build 	mkdir $DIR &&\
:info:build 	tar -C $DIR --strip-components=1 -xzf standard-RAxML-8.0.26.tar.gz &&\
:info:build 	arb_sed -i 's/-march=native//' $DIR/Makefile*)
:info:build touch unpack.PTHREADS.stamp -r standard-RAxML-8.0.26.tar.gz	
:info:build MAKEFLAGS= /Applications/Xcode.app/Contents/Developer/usr/bin/make -C builddir.SSE3.PTHREADS -f Makefile.SSE3.PTHREADS.gcc
:info:build gcc  -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops     -c -o axml.o axml.c
:info:build gcc -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -c -o axml.o axml.c
:info:build gcc: Error: You should be using ${configure.cc}
:info:build See https://trac.macports.org/wiki/UsingTheRightCompiler
:info:build make[6]: *** [axml.o] Error 1
:info:build make[5]: *** [/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/trunk/bin/raxmlHPC8-SSE3.PTHREADS] Error 2
:info:build make[5]: Leaving directory `/opt/local/var/macports/build/_Users_cottrell_Documents_Programming_MacPorts_ports_science_arb/arb/work/trunk/GDE/RAxML8'
:info:build make[4]: *** [RAxML8/RAxML8.dummy] Error 1
:info:build make[4]: *** Waiting for unfinished jobs....

[epruesse]

This was due to a typo in the Makefile. r12994 should fix it.

RAxML comes with Makefiles for mac, which weren't used. It should now read

build MAKEFLAGS= /Applications/Xcode.app/Contents/Developer/usr/bin/make -C builddir.SSE3.PTHREADS -f Makefile.SSE3.PTHREADS.mac

instead of

build MAKEFLAGS= /Applications/Xcode.app/Contents/Developer/usr/bin/make -C builddir.SSE3.PTHREADS -f Makefile.SSE3.PTHREADS.gcc

Could you try again?

(If you don't want to update, the change was just to change ifeq (($DARWIN),1) to ifeq ($(DARWIN),1) in GDE/RAxML8/Makefile.

[epruesse]

I tried to do some patching myself, but I can't patch the RAxML code because it is packed in a compressed file and only later unpacked during the build.

Yes. I figured it'd be better to follow the general practice in distributions: upstream tarball + patches instead of maintaining a copy of the source in a VCS. The makefile doesn't support patches yet, because they weren't really necessary. If there really is something to patch in RAxML, I'd patch on github, ask Alexis to pull the changes and then update the tarball to a new RAxML release.

[mcottrell]

ARB now builds and runs on MacPorts? with r12994. Thanks for finding that typo.

[westram]

mark changes that got fixed after arb 6.0.x

[westram]

Milestone renamed