search

xflouris / libpll-2

Phylogenetic Likelihood Library 2 - experimental
GNU Affero General Public License v3.0
9 stars 12 forks source link

build not working with bison `3.8` (solved: use bison `3.8.2`) #23

Closed dlaehnemann closed 1 year ago

dlaehnemann commented 1 year ago

It seems like bison in its latest version (3.8) creates incorrect / incompatible parse_utree files. I'm just guessing here, but this might be due to breaking changes in 3.8. For me, it works with version 3.4 (intermediate versions are not available on conda-forge, so I can't quickly test them).

So as a quick fix, it might be worth recommending a lower bison version in the README.md here, and also in projects depending on this library (I came across this in raxml-ng). And I have no clue how to properly fix this, sorry.

Here's a reproducible way of triggering this:

# set up build dependencies
mamba create -n libpll_2_build bison=3.8 flex autoconf automake libtool gcc
mamba activate libpll_2_build
# Instructions from the README.md
git clone https://github.com/xflouris/libpll.git
cd libpll
./autogen.sh
./configure
make

It throws the error below. Note, however, that changing the version to bison=3.4 allows the make to succeed.

/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_utree.lo -MD -MP -MF .deps/libpll_la-parse_utree.Tpo -c -o libpll_la-parse_utree.lo `test -f 'parse_utree.c' || echo './'`parse_utree.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_utree.lo -MD -MP -MF .deps/libpll_la-parse_utree.Tpo -c parse_utree.c  -fPIC -DPIC -o .libs/libpll_la-parse_utree.o
parse_utree.c:297:6: error: conflicting types for 'pll_utree_error'; have 'void(const char *)'
  297 | void pll_utree_error (const char *msg);
      |      ^~~~~~~~~~~~~~~
parse_utree.y:139:13: note: previous definition of 'pll_utree_error' with type 'void(pll_unode_t *, const char *)' {aka 'void(struct pll_unode_s *, const char *)'}
  139 | static void pll_utree_error(pll_unode_t * node, const char * s)
      |             ^~~~~~~~~~~~~~~
parse_utree.c: In function 'pll_utree_parse':
parse_utree.c:1774:18: warning: passing argument 1 of 'pll_utree_error' from incompatible pointer type [-Wincompatible-pointer-types]
 1774 |         yyerror (tree, yymsgp);
      |                  ^~~~
      |                  |
      |                  struct pll_unode_s *
parse_utree.c:297:35: note: expected 'const char *' but argument is of type 'struct pll_unode_s *'
  297 | void pll_utree_error (const char *msg);
      |                       ~~~~~~~~~~~~^~~
parse_utree.c:70:25: error: too many arguments to function 'pll_utree_error'
   70 | #define yyerror         pll_utree_error
      |                         ^~~~~~~~~~~~~~~
parse_utree.c:1774:9: note: in expansion of macro 'yyerror'
 1774 |         yyerror (tree, yymsgp);
      |         ^~~~~~~
parse_utree.c:297:6: note: declared here
  297 | void pll_utree_error (const char *msg);
      |      ^~~~~~~~~~~~~~~
parse_utree.c:1888:12: warning: passing argument 1 of 'pll_utree_error' from incompatible pointer type [-Wincompatible-pointer-types]
 1888 |   yyerror (tree, YY_("memory exhausted"));
      |            ^~~~
      |            |
      |            struct pll_unode_s *
parse_utree.c:297:35: note: expected 'const char *' but argument is of type 'struct pll_unode_s *'
  297 | void pll_utree_error (const char *msg);
      |                       ~~~~~~~~~~~~^~~
parse_utree.c:70:25: error: too many arguments to function 'pll_utree_error'
   70 | #define yyerror         pll_utree_error
      |                         ^~~~~~~~~~~~~~~
parse_utree.c:1888:3: note: in expansion of macro 'yyerror'
 1888 |   yyerror (tree, YY_("memory exhausted"));
      |   ^~~~~~~
parse_utree.c:297:6: note: declared here
  297 | void pll_utree_error (const char *msg);
      |      ^~~~~~~~~~~~~~~
parse_utree.y: At top level:
parse_utree.y:139:13: warning: 'pll_utree_error' defined but not used [-Wunused-function]
  139 | static void pll_utree_error(pll_unode_t * node, const char * s)
      |             ^~~~~~~~~~~~~~~
make[2]: *** [Makefile:856: libpll_la-parse_utree.lo] Error 1
make[2]: Leaving directory '/path/to/libpll/src'
make[1]: *** [Makefile:406: all-recursive] Error 1
make[1]: Leaving directory '/path/to/libpll'
make: *** [Makefile:338: all] Error 2
dlaehnemann commented 1 year ago

I just saw, that pinning to bison==3.4 was also the fix for the raxml-ng recipe over at bioconda...

tillea commented 1 year ago

Am Fri, Apr 21, 2023 at 10:14:08AM -0700 schrieb David Laehnemann:

I just saw, that pinning to bison==3.4 was also the fix for the raxml-ng recipe over at bioconda...

Thanks for the hint to pin bison to some lower version. Unfortunately this does not solve my problem since I need to work with the version provided by the system which in Debian is currently 3.8.2. Do you have any other recommendation? Kind regards, Andreas.

dlaehnemann commented 1 year ago

I would recommend using mamba/conda to install the dependencies into an isolated environment with the command I provide above (mamba create ...) and then activate that environment (mamba activate ...) to run the build with all the dependencies you installed into it. You don't need root access to install stuff with mamba/conda (or mamba/conda itself), so this should work on any system. Also, from what I understand, none of these dependencies are needed at runtime, so the mamba/conda environment should only need to be activated during the build (howver, this is only true for libpll-2 -- some further dependencies for raxml-ng are also needed at runtime, in case raxml-ng was also the case that broke for you).

The installation of mamba itself is also very quick and easy, I recommend this guide:

https://github.com/conda-forge/miniforge#install

You should be up and running in 5 minutest. And if you're the suspicious kind, have a read through the install scripts... ;)

dlaehnemann commented 1 year ago

BTW, it took me weeks to finally track this down. So I'll also document this over at raxml-ng to save others the trouble...

amkozlov commented 1 year ago

Hi David,

seems like you cloned libpll and not libpll-2.

This repository is libpll-2, which is also the version used by raxml-ng (and probably most other tools). And libpll-2 does compile with bison 3.8 (I just tested it).

dlaehnemann commented 1 year ago

You are right, with the above commands I seem to have cloned libpll instead of libpll-2. I was simply following the compilation instructions from the README.md, that point to libpll instead of libpll-2. I created a quick pull request #24 with the docs updates. ;)

However, I can reproduce the same error with libpll-2, namely with these commands:

mamba create -n libpll_2_build bison=3.8 flex autoconf automake libtool gcc
mamba activate libpll_2_build
git clone https://github.com/xflouris/libpll-2.git
cd libpll-2/
./autogen.sh
./configure
make

This leads to the error:

/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_utree.lo -MD -MP -MF .deps/libpll_la-parse_utree.Tpo -c -o libpll_la-parse_utree.lo `test -f 'parse_utree.c' || echo './'`parse_utree.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_utree.lo -MD -MP -MF .deps/libpll_la-parse_utree.Tpo -c parse_utree.c  -fPIC -DPIC -o .libs/libpll_la-parse_utree.o
parse_utree.c:306:6: error: conflicting types for 'pll_utree_error'; have 'void(const char *)'
  306 | void pll_utree_error (const char *msg);
      |      ^~~~~~~~~~~~~~~
parse_utree.y:147:13: note: previous definition of 'pll_utree_error' with type 'void(pll_unode_t *, const char *)' {aka 'void(struct pll_unode_s *, const char *)'}
  147 | static void pll_utree_error(pll_unode_t * node, const char * s)
      |             ^~~~~~~~~~~~~~~
parse_utree.c: In function 'pll_utree_parse':
parse_utree.c:1806:18: warning: passing argument 1 of 'pll_utree_error' from incompatible pointer type [-Wincompatible-pointer-types]
 1806 |         yyerror (tree, yymsgp);
      |                  ^~~~
      |                  |
      |                  struct pll_unode_s *
parse_utree.c:306:35: note: expected 'const char *' but argument is of type 'struct pll_unode_s *'
  306 | void pll_utree_error (const char *msg);
      |                       ~~~~~~~~~~~~^~~
parse_utree.c:70:25: error: too many arguments to function 'pll_utree_error'
   70 | #define yyerror         pll_utree_error
      |                         ^~~~~~~~~~~~~~~
parse_utree.c:1806:9: note: in expansion of macro 'yyerror'
 1806 |         yyerror (tree, yymsgp);
      |         ^~~~~~~
parse_utree.c:306:6: note: declared here
  306 | void pll_utree_error (const char *msg);
      |      ^~~~~~~~~~~~~~~
parse_utree.c:1920:12: warning: passing argument 1 of 'pll_utree_error' from incompatible pointer type [-Wincompatible-pointer-types]
 1920 |   yyerror (tree, YY_("memory exhausted"));
      |            ^~~~
      |            |
      |            struct pll_unode_s *
parse_utree.c:306:35: note: expected 'const char *' but argument is of type 'struct pll_unode_s *'
  306 | void pll_utree_error (const char *msg);
      |                       ~~~~~~~~~~~~^~~
parse_utree.c:70:25: error: too many arguments to function 'pll_utree_error'
   70 | #define yyerror         pll_utree_error
      |                         ^~~~~~~~~~~~~~~
parse_utree.c:1920:3: note: in expansion of macro 'yyerror'
 1920 |   yyerror (tree, YY_("memory exhausted"));
      |   ^~~~~~~
parse_utree.c:306:6: note: declared here
  306 | void pll_utree_error (const char *msg);
      |      ^~~~~~~~~~~~~~~
parse_utree.y: At top level:
parse_utree.y:147:13: warning: 'pll_utree_error' defined but not used [-Wunused-function]
  147 | static void pll_utree_error(pll_unode_t * node, const char * s)
      |             ^~~~~~~~~~~~~~~
make[2]: *** [Makefile:859: libpll_la-parse_utree.lo] Error 1
make[2]: Leaving directory '/path/to/libpll-2/src'
make[1]: *** [Makefile:406: all-recursive] Error 1
make[1]: Leaving directory '/path/to/libpll-2'
make: *** [Makefile:338: all] Error 2

This looks like the same problem.

So maybe you are using some slightly different version of bison 3.8 than the one conda-forge provides for me? The above environment creation got me:

bison                        3.8  h9c3ff4c_0        conda-forge/linux-64

And the version given by the tool is:

$ bison --version
bison (GNU Bison) 3.8
Written by Robert Corbett and Richard Stallman.

Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Can you try with these instructions and so we can see whether this is a problem with the version on conda-forge?

amkozlov commented 1 year ago

Good point, thanks!

I tested with bison 3.8.2 which comes with Ubuntu 22.04: 

$ bison --version
bison (GNU Bison) 3.8.2
Written by Robert Corbett and Richard Stallman.

Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
dlaehnemann commented 1 year ago

OK, seems like the conda-forge recipe for bison could do with an update to 3.8.2. I'll try to get that rolling. If that then fixes the compilation issue here, I'll close this issue.

dlaehnemann commented 1 year ago

Alright, the bison update on conda-forge to version 3.8.2 has been merged (and is available to install): https://github.com/conda-forge/bison-feedstock/pull/31

And with this version, I can confirm that the build / compiling works with the following setup (as above, just bison pinned to the newest 3.8.2:

mamba create -n libpll_2_build bison=3.8.2 flex autoconf automake libtool gcc
mamba activate libpll_2_build
git clone https://github.com/xflouris/libpll-2.git
cd libpll-2/
./autogen.sh
./configure
make