Compiling poy4 ?

Clement Schneider

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Jul 19, 2016, 12:14:11 PM7/19/16

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Hello everyone.

I wanted to run some tests using older/newer version of poy4 and 5 and I am not able to compile poy4.

I got the following sources:

poy-4.1.2 on http://www.amnh.org
poy-4.1.2 (git) on https://github.com/amnh/POY4

I tried to compile with Ocaml 3.12.1 and 4.01

Compiling with
./configure --enable-interface=flat --enable-mpi CC=mpicc CFLAGS="-msse3 -O3"

Using Ocaml 3.12.1, compiled from sources.

poy-4.1.2
on configure:
----------------
checking for OCaml version... 3.12.1
no
configure: error: in `/Data/clement/bin/old_poy/sources/poy-4.1.2/src':
configure: error: POY requires OCaml version 3.10.2 or later to compile. Please upgrade to the latest version. (You can get it from http://www.ocaml.org and follow their compilation instructions. It's really easy.)
See `config.log' for more details.
----------------
Okay those sources won't accept any versions of Ocaml above 3.10.2

poy-4.1.2 (git)
configure is now ok with Ocaml 3.12.1, go for the make :o)
----------------
ukk.checkp.c:(.text+0x1350): undefined reference to `seq_prepend'
./libpoycside.a(ukk.checkp.o):ukk.checkp.c:(.text+0x135f): more undefined references to `seq_prepend' follow
collect2: error: ld returned 1 exit status
File "caml_startup", line 1, characters 0-1:
Error: Error during linking
Command exited with code 2.
Makefile:67: recipe for target 'poy.native' failed
make[1]: *** [poy.native] Error 10
make[1]: Leaving directory '/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src'
make: *** [poy.native] Error 2
Makefile:69: recipe for target 'poy.native' failed
------------------

moving to Ocaml 4.01 compiled from sources

poy-4.1.2 (git)
--------------------
ukk.checkp.c:(.text+0x1350): undefined reference to `seq_prepend'
./libpoycside.a(ukk.checkp.o):ukk.checkp.c:(.text+0x135f): more undefined references to `seq_prepend' follow
collect2: error: ld returned 1 exit status
File "caml_startup", line 1:
Error: Error during linking
Command exited with code 2.
make[1]: *** [poy.native] Error 10
Makefile:67: recipe for target 'poy.native' failed
make[1]: Leaving directory '/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src'
make: *** [poy.native] Error 2
Makefile:69: recipe for target 'poy.native' failed
---------------------

at this point, I get I'm missing something if I want to compile poy4. But I don't know what. I append below the stdout for configure, I don't see anything important.

I' am not able to get poy4 binaries parallel for linux x64. Any ideas why it failed to compile ? Maybe someone could directly provide me the binaries ?

All the best
Clément

----
stdout for configure

checking whether make sets $(MAKE)... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gcc... mpicc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking for hg... hg
checking for ocamlc.opt... ocamlc.opt
checking for ocamlbuild.native... ocamlbuild.native
checking for ocaml... ocaml
configure: creating ./config.status
config.status: creating Makefile
=== configuring in src (/home/clement/bin/old_poy/sources/poy4-release5-05-07/src)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--enable-interface=flat' '--enable-mpi' 'CC=mpicc' 'CFLAGS=-msse3 -O3' --cache-file=/dev/null --srcdir=.
checking for gcc... mpicc
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking for hg... hg
checking for xslt-config... xslt-config
Finished xslt crap
checking how to run the C preprocessor... mpicc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for ocaml... ocaml
checking for ocamlc.opt... ocamlc.opt
checking for ocamlyacc.opt... no
checking for ocamlyacc... ocamlyacc
checking for ocamllex.opt... ocamllex.opt
checking for ocamlopt.opt... ocamlopt.opt
checking for ocamldep.opt... ocamldep.opt
checking for ocamlbuild.native... ocamlbuild.native
checking for camlp4orf... camlp4orf
checking for ocamlmktop... ocamlmktop
checking for OCaml version... 4.01.0
checking whether we need to add --no-as-needed linking option... yes
checking if OCaml supports dynamic linking in this architecture... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking whether mpicc needs -traditional... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking for library containing zlibVersion... -lz
checking for floor... no
checking for gettimeofday... yes
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for sin... no
checking for exp... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating _tags
config.status: creating myocamlbuild.ml
config.status: creating buildNumber.ml
config.status: creating compileFlags.ml
config.status: creating config.h

Ward C Wheeler

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Jul 19, 2016, 3:26:28 PM7/19/16

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Do you specifically need POY? Could you use POY5?

W

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Ward Wheeler
Division of Invertebrate Zoology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192
USA
http://www.amnh.org/our-research/staff-directory/ward-wheeler

http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download

Clement Schneider

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Jul 19, 2016, 5:20:17 PM7/19/16

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Hello Ward,

The thing is I'm trying to repeat 3 years old analyses (with a few additional taxa) and I'm running into some issues with poy5.1.1 (compiled on my computer and on my institution cluster), being analyses ending with segmentation fault. However only a small subset of my scripts crashes (same scripts but different input data and/or sankoff matrices).

Additionally I'm under the impression that the scripts' execution is longer than it used to require (but I'm not sure).

Before submitting the whole case here, I wanted to try a few runs with anterior versions of poy (and ocaml) and particularly poy4 (I used 3 years ago). And also trying to rule out human error on my side.

That is how I stepped on the 'poy4 unable to compile' issue.

W

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Ward C Wheeler

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Jul 19, 2016, 6:01:31 PM7/19/16

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Clement,

Could you try this source code and perhaps these binaries (for POY4).

http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download

W

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Clement Schneider

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Jul 20, 2016, 11:46:00 AM7/20/16

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The source code at http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download
cannot configure for Ocaml > 3.10.2 (I tried to compile with 3.10.2 and get the same kind of error I reported in my first post).

I also tried the lastest release on git (poy4.1.2 release 5) that take Ocaml >= 3.10.2 but with compilation error (see my first post).
I have no problem compiling poy5.1.1.

Yes I can use the pre-compiled binaries for poy4, but only the x86 without parallel support are released for linux.

Clément

Ward Wheeler

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Jul 20, 2016, 11:56:48 AM7/20/16

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And you need the parallel? I have OS X binaries for parallel and sequential--any chance that would do?

W

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Nick Lucaroni

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Jul 20, 2016, 11:59:50 AM7/20/16

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Definitely pull the source code from the git repos instead of the AMNH site --since I left, I was able to make updates to the codebase, but not update the site with new versions of the source.

I hadn't experienced linking (the collect2 : ld exit status code ... error you got) issues when I was testing. Was there more information above that? Possibly in the loooong list of output that a sub-component failed in compilation but didn't fail the build properly?

What c compiler / toolchain are you using? gcc? clang? what version?

Are you running the configure / build within the src directory?

--

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Clement Schneider

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Jul 20, 2016, 12:28:21 PM7/20/16

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Thanks for the tip Ward, I know that windows and Mac OS X binaries come with parallel on. It is not very practical for me but I can use this as a last resort.

Nicholas
I launched configure and make from the basal directory, stdout of make start with "cd src; \" so I guess it is ok, but I will try to configure and make from ./src --> I just did it, it is the same error

>gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.1) 5.4.0 20160609
Is the "toolchain" something different than the compiler ? (my knowledge is rather poor)

Because poy compilation always issued a lot of warnings without apparent importance, I don't really know if there is something relevant in the stdout. I post the whole thing here:

ocamlbuild.native poy.native
Finished, 1 target (0 cached) in 00:00:00.
+ /usr/local/bin/ocamlc.opt -ccopt -I -ccopt /usr/include/malloc -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSENCURSES -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -c grappa/all_sorting_reversals.c
grappa/all_sorting_reversals.c: In function ‘find_all_sorting_reversals’:
grappa/all_sorting_reversals.c:145:16: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                ( void * ) i );
                ^
grappa/all_sorting_reversals.c:167:16: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                ( void * ) i );
                ^
grappa/all_sorting_reversals.c:179:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
             j = ( int ) list_get ( &mem->conn_comp[i].cyclelist, 0 );
                 ^
grappa/all_sorting_reversals.c:299:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 a = ( int ) list_get ( &mem->cyclelist[i], j );
                     ^
grappa/all_sorting_reversals.c:300:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 b = ( int ) list_get ( &mem->cyclelist[c + 1 + i], k );
                     ^
grappa/all_sorting_reversals.c:351:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                         a = ( int ) list_get ( &mem->
                             ^
grappa/all_sorting_reversals.c:354:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                         b = ( int ) list_get ( &mem->
                             ^
grappa/all_sorting_reversals.c:460:43: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                 cyclelist[( int )
                                           ^
grappa/all_sorting_reversals.c:465:43: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                 cyclelist[( int )
                                           ^
grappa/all_sorting_reversals.c:473:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                     a = ( int ) list_get ( edges1, k );
                                         ^
grappa/all_sorting_reversals.c:474:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                     b = ( int ) list_get ( edges2, k2 );
                                         ^
grappa/all_sorting_reversals.c:497:35: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( mem->mhurdles, ( void * ) i );
                                   ^
grappa/all_sorting_reversals.c:515:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 h1 = ( int ) list_get ( mem->mhurdles, i );
                      ^
grappa/all_sorting_reversals.c:516:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 h2 = ( int ) list_get ( mem->mhurdles, j );
                      ^
grappa/all_sorting_reversals.c:565:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                     oc = ( int ) list_get ( &ocs[i], k );
                          ^
grappa/all_sorting_reversals.c:569:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                         h = ( int ) list_get ( mem->mhurdles, j );
                             ^
grappa/all_sorting_reversals.c:618:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                         int o1 = ( int ) list_get ( &ocs[i], k );
                                  ^
grappa/all_sorting_reversals.c:621:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             int o2 = ( int ) list_get ( &ocs[j], k2 );
                                      ^
grappa/all_sorting_reversals.c:644:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                         push ( &non_separated_ocs, ( void * ) i );
                                                    ^
grappa/all_sorting_reversals.c:658:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                         int h = ( int ) list_get ( mem->mhurdles, i );
                                 ^
grappa/all_sorting_reversals.c:659:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                         push ( &to_merge1, ( void * ) h );
                                            ^
grappa/all_sorting_reversals.c:664:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             int oc = ( int ) list_get ( &ocs[lidx[h]], j );
                                      ^
grappa/all_sorting_reversals.c:665:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                             push ( &to_merge1, ( void * ) oc );
                                                ^
grappa/all_sorting_reversals.c:672:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                    ( void * ) mem->conn_comp[h].anchor );
                                    ^
grappa/all_sorting_reversals.c:683:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                 push ( &to_merge2, ( void * ) j );
                                                    ^
grappa/all_sorting_reversals.c:693:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                 ( int ) list_get ( &non_separated_ocs, j );
                                 ^
grappa/all_sorting_reversals.c:698:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                 push ( &to_merge2, ( void * ) bc );
                                                    ^
grappa/all_sorting_reversals.c:703:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             int c1 = ( int ) list_get ( &to_merge1, j );
                                      ^
grappa/all_sorting_reversals.c:706:42: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                 int c2 = ( int ) list_get ( &to_merge2, k );
                                          ^
grappa/all_sorting_reversals.c:730:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                         int hrdl = ( int ) list_get ( mem->mhurdles, i );
                                    ^
grappa/all_sorting_reversals.c:734:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                    ( void * ) mem->conn_comp[hrdl].anchor );
                                    ^
grappa/all_sorting_reversals.c:739:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                             push ( &tmpl, ( void * ) hrdl );
                                           ^
grappa/all_sorting_reversals.c:758:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                         push ( &tmpl, ( void * ) j );
                                                       ^
grappa/all_sorting_reversals.c:766:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                         push ( &tmpl, ( void * ) j );
                                                       ^
grappa/all_sorting_reversals.c:775:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                 ( int ) list_get ( &non_separated_ocs, j );
                                 ^
grappa/all_sorting_reversals.c:783:47: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                 push ( &tmpl, ( void * ) bc );
                                               ^
grappa/all_sorting_reversals.c:790:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             if ( ( int )
                                  ^
grappa/all_sorting_reversals.c:797:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                     ( int ) list_get ( &mem->conn_comp[hrdl].
                                     ^
grappa/all_sorting_reversals.c:800:47: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                                 push ( &tmpl, ( void * ) partner );
                                               ^
grappa/all_sorting_reversals.c:816:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             int comp = ( int ) list_get ( &tmpl, j );
                                        ^
grappa/all_sorting_reversals.c:833:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                         ( int ) list_get ( &ocs[lidx[hrdl]],
                                         ^
grappa/all_sorting_reversals.c:856:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                     ( int ) list_get ( &ocs[lidx[hrdl]], k );
                                     ^
grappa/all_sorting_reversals.c:862:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                         ( int ) list_get ( &ocs[lidx[hrdl]],
                                         ^
grappa/all_sorting_reversals.c: In function ‘find_connected_components’:
grappa/all_sorting_reversals.c:952:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( mem->stack, ( void * ) mem->cc_e[i] );
                                ^
grappa/all_sorting_reversals.c:953:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         top = ( int ) peek_stack ( mem->stack );
               ^
grappa/all_sorting_reversals.c:965:19: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
             top = ( int ) peek_stack ( mem->stack );
                   ^
grappa/all_sorting_reversals.c: In function ‘build_uoc_list’:
grappa/all_sorting_reversals.c:1027:30: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( uoc_list, ( void * ) current );
                              ^
grappa/all_sorting_reversals.c: In function ‘find_superhurdles’:
grappa/all_sorting_reversals.c:1050:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
     prevlbl = ( int ) list_get ( uoc_list, list_size ( uoc_list ) - 1 );
               ^
grappa/all_sorting_reversals.c:1058:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         currentlbl = ( int ) list_get ( uoc_list, i );
                      ^
grappa/all_sorting_reversals.c:1067:31: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                               ( void * ) ( idx[currentlbl] ) ) )
                               ^
grappa/all_sorting_reversals.c:1073:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( &adj_list[idx[prevlbl]], ( void * ) idx[currentlbl] );
                                             ^
grappa/all_sorting_reversals.c:1074:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( &adj_list[idx[currentlbl]], ( void * ) idx[prevlbl] );
                                                ^
grappa/all_sorting_reversals.c:1093:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         v = ( int ) pop_stack ( &S );
             ^
grappa/all_sorting_reversals.c:1100:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 n = ( int ) list_get ( &adj_list[v], i );
                     ^
grappa/all_sorting_reversals.c:1105:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                         push ( &cycles[n], ( void * ) ncycles );
                                            ^
grappa/all_sorting_reversals.c:1110:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                             push ( &cycles[u], ( void * ) ncycles );
                                                ^
grappa/all_sorting_reversals.c:1115:56: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                             push ( &three_cycles_memb, ( void * ) v );
                                                        ^
grappa/all_sorting_reversals.c:1120:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                         push ( &S, ( void * ) n );
                                    ^
grappa/all_sorting_reversals.c:1165:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 n = ( int ) list_get ( &adj_list[i], 0 );
                     ^
grappa/all_sorting_reversals.c:1193:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         u[0] = ( int ) list_get ( &three_cycles_memb, i );
                ^
grappa/all_sorting_reversals.c:1229:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                            ( void * ) label[w] );
                            ^
grappa/all_sorting_reversals.c:1231:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                            ( void * ) label[v] );
                            ^
grappa/all_sorting_reversals.c:1254:25: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                     j = ( int ) list_get ( &adj_list[i], 0 );
                         ^
grappa/all_sorting_reversals.c:1283:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             x1 = label[( int ) list_get ( &adj_list[i], 0 )];
                                        ^
grappa/all_sorting_reversals.c:1284:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             x2 = label[( int ) list_get ( &adj_list[j], 0 )];
                                        ^
grappa/all_sorting_reversals.c:1296:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             int newj = ( int ) list_get ( &adj_list[j], 0 );
                                        ^
grappa/all_sorting_reversals.c:1300:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                 j = ( int ) list_get ( &adj_list[j], 1 );
                                     ^
grappa/all_sorting_reversals.c: In function ‘find_single_hurdle’:
grappa/all_sorting_reversals.c:1327:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         v = ( int ) list_get ( &adj_list[u], i );
             ^
grappa/all_sorting_reversals.c:1345:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         next = ( int ) list_get ( &adj_list[v], 0 ) == prev ?
                ^
grappa/all_sorting_reversals.c:1346:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
             ( int ) list_get ( &adj_list[v], 1 ) :
             ^
grappa/all_sorting_reversals.c:1347:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
             ( int ) list_get ( &adj_list[v], 0 );
             ^
grappa/all_sorting_reversals.c: In function ‘count_hurdles_after_reversal’:
grappa/all_sorting_reversals.c:1687:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         label = ( int ) list_get ( V, i );
                 ^
grappa/all_sorting_reversals.c: In function ‘new_nhurdles_plus_nfortresses_cc’:
grappa/all_sorting_reversals.c:1791:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( &mem->comp_grey_edges[comp], ( void * ) mem->upi_cpy[i] );
                                                 ^
grappa/all_sorting_reversals.c: In function ‘add_all_merging_reversals’:
grappa/all_sorting_reversals.c:1860:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                    ( int ) list_get ( &c1->cyclelist, i )];
                                    ^
grappa/all_sorting_reversals.c:1863:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                                    ( int ) list_get ( &c2->cyclelist, j )];
                                    ^
grappa/all_sorting_reversals.c:1868:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             a = ( int ) list_get ( edges1, k );
                                 ^
grappa/all_sorting_reversals.c:1869:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                             b = ( int ) list_get ( edges2, k2 );
                                 ^
grappa/all_sorting_reversals.c: In function ‘add_all_cutting_reversals’:
grappa/all_sorting_reversals.c:1892:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         edges = &cyclelist[( int ) list_get ( &cc->cyclelist, j )];
                            ^
grappa/all_sorting_reversals.c:1897:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 a = ( int ) list_get ( edges, k );
                     ^
grappa/all_sorting_reversals.c:1898:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 b = ( int ) list_get ( edges, k2 );
                     ^
grappa/all_sorting_reversals.c: In function ‘form_double_superhurdle’:
grappa/all_sorting_reversals.c:1940:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
            ( int ) list_get ( &conn_comp[h1].double_superhurdle_partners,
            ^
grappa/all_sorting_reversals.c:1943:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
               && ( int ) list_get ( &conn_comp[h1].
                  ^
grappa/all_sorting_reversals.c: In function ‘find_separating_hurdles’:
grappa/all_sorting_reversals.c:2219:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 comp = ( int ) pop_stack ( &tmpl );
                        ^
grappa/all_sorting_reversals.c:2222:40: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                 push ( &separated_ocs, ( void * ) comp );
                                        ^
grappa/all_sorting_reversals.c:2223:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
                 push ( &separating_hurdles, ( void * ) currenth );
                                             ^
grappa/all_sorting_reversals.c:2248:25: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
                 int c = ( int ) pop_stack ( &tmpl );
                         ^
grappa/all_sorting_reversals.c:2324:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( &tmpl, ( void * ) comp );
                           ^
grappa/all_sorting_reversals.c:2347:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
             oc = ( int ) list_get ( &separated_ocs, i );
                  ^
grappa/all_sorting_reversals.c:2349:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
             h = ( int ) list_get ( &separating_hurdles, i );
                 ^
grappa/all_sorting_reversals.c:2357:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
             push ( &( *ocs )[j], ( void * ) oc );
                                  ^
+ /usr/local/bin/ocamlc.opt -ccopt -I -ccopt /usr/include/malloc -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSENCURSES -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -c algn.c
algn.c:3279:13: warning: ‘fill_moved’ is static but used in inline function ‘algn_fill_cube_ukk’ which is not static
             fill_moved (s3_len, prev_m - 1, upper_m - 1, diag_m - 1, s1gs3, \
             ^
algn.c:3093:13: warning: ‘fill_moved’ is static but used in inline function ‘algn_fill_cube’ which is not static
             fill_moved (s3_len, prev_m - 1, upper_m - 1, diag_m - 1, s1gs3, \
             ^
+ /usr/local/bin/ocamlc.opt -ccopt -I -ccopt /usr/include/malloc -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSENCURSES -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -c ukk.checkp.c
In file included from ukk.checkp.c:33:0:
seq.h:126:1: warning: inline function ‘seq_set’ declared but never defined
seq_set (seqt a, int p, SEQT v);
^
seq.h:118:1: warning: inline function ‘seq_get’ declared but never defined
seq_get (const seqt a, int p);
^
seq.h:109:1: warning: inline function ‘seq_get_end’ declared but never defined
seq_get_end (const seqt a);
^
seq.h:100:1: warning: inline function ‘seq_get_head’ declared but never defined
seq_get_head (const seqt a);
^
seq.h:91:1: warning: inline function ‘seq_get_begin’ declared but never defined
seq_get_begin (const seqt a);
^
seq.h:83:1: warning: inline function ‘seq_get_len’ declared but never defined
seq_get_len (const seqt a);
^
seq.h:75:1: warning: inline function ‘seq_prepend’ declared but never defined
seq_prepend (seqt a, SEQT v);
^
seq.h:68:1: warning: inline function ‘seq_get_cap’ declared but never defined
seq_get_cap (const seqt a);
^
In file included from seq.h:26:0,
                 from ukk.checkp.c:33:
array_pool.h:50:1: warning: inline function ‘pool_alloc’ declared but never defined
pool_alloc (struct pool *p, void *update_item);
^
+ /usr/local/bin/ocamlc.opt -ccopt -I -ccopt /usr/include/malloc -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSENCURSES -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -c ukkCommon.c
In file included from ukkCommon.c:41:0:
seq.h:126:1: warning: inline function ‘seq_set’ declared but never defined
seq_set (seqt a, int p, SEQT v);
^
seq.h:118:1: warning: inline function ‘seq_get’ declared but never defined
seq_get (const seqt a, int p);
^
seq.h:109:1: warning: inline function ‘seq_get_end’ declared but never defined
seq_get_end (const seqt a);
^
seq.h:100:1: warning: inline function ‘seq_get_head’ declared but never defined
seq_get_head (const seqt a);
^
seq.h:91:1: warning: inline function ‘seq_get_begin’ declared but never defined
seq_get_begin (const seqt a);
^
seq.h:83:1: warning: inline function ‘seq_get_len’ declared but never defined
seq_get_len (const seqt a);
^
seq.h:75:1: warning: inline function ‘seq_prepend’ declared but never defined
seq_prepend (seqt a, SEQT v);
^
seq.h:68:1: warning: inline function ‘seq_get_cap’ declared but never defined
seq_get_cap (const seqt a);
^
In file included from seq.h:26:0,
                 from ukkCommon.c:41:
array_pool.h:50:1: warning: inline function ‘pool_alloc’ declared but never defined
pool_alloc (struct pool *p, void *update_item);
^
+ /usr/local/bin/ocamlopt.opt -c -annot -I +camlp4 -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -pp 'camlp4orf poyExtension.cmo -DUSE_NATIVEDYNLINK    -DUSENCURSES        ' -I camlpdf-0.3 -I utils -I plugins -I grappa -I gz-0.5.7 -I ocamlmpi -o sequence.cmx sequence.ml
File "sequence.ml", line 1975, characters 34-36:
Warning 3: deprecated feature: operator (or); you should use (||) instead
File "sequence.ml", line 1965, characters 33-35:
Warning 3: deprecated feature: operator (or); you should use (||) instead
+ /usr/local/bin/ocamlopt.opt -c -annot -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I grappa -I gz-0.5.7 -I ocamlmpi -o chromAli.cmx chromAli.ml
File "chromAli.ml", line 590, characters 18-20:
Warning 3: deprecated feature: operator (or); you should use (||) instead
+ /usr/local/bin/ocamlopt.opt -c -annot -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I grappa -I gz-0.5.7 -I ocamlmpi -o genomeAli.cmx genomeAli.ml
File "genomeAli.ml", line 864, characters 25-27:
Warning 3: deprecated feature: operator (or); you should use (||) instead
+ /usr/local/bin/ocamlopt.opt -c -annot -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I grappa -I gz-0.5.7 -I ocamlmpi -o queues.cmx queues.ml
File "queues.ml", line 525, characters 40-57:
Warning 20: this argument will not be used by the function.
File "queues.ml", line 526, characters 40-55:
Warning 20: this argument will not be used by the function.
File "queues.ml", line 527, characters 40-42:
Warning 20: this argument will not be used by the function.
File "queues.ml", line 527, characters 43-45:
Warning 20: this argument will not be used by the function.
File "queues.ml", line 527, characters 46-51:
Warning 20: this argument will not be used by the function.
File "queues.ml", line 527, characters 52-54:
Warning 20: this argument will not be used by the function.
File "queues.ml", line 528, characters 40-47:
Warning 20: this argument will not be used by the function.
+ /usr/local/bin/ocamlopt.opt -c -annot -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I grappa -I gz-0.5.7 -I ocamlmpi -o impliedAlignment.cmx impliedAlignment.ml
File "impliedAlignment.ml", line 2256, characters 41-50:
Warning 26: unused variable apply_map.
+ /usr/local/bin/ocamlopt.opt -c -annot -I +camlp4 -cc gcc -ccopt -fPIC -ccopt -g -ccopt -O2 -pp 'camlp4orf poyExtension.cmo -DUSE_NATIVEDYNLINK    -DUSENCURSES        ' -I camlpdf-0.3 -I utils -I plugins -I grappa -I gz-0.5.7 -I ocamlmpi -o scripting.cmx scripting.ml
File "scripting.ml", line 2007, characters 12-13:
Warning 3: deprecated feature: operator (&); you should use (&&) instead
+ /usr/local/bin/ocamlopt.opt dynlink.cmxa unix.cmxa str.cmxa bigarray.cmxa -I +camlp4 camlp4fulllib.cmxa -cclib -lz -cclib -lpoycside -cclib -L. -cclib -Wl,--no-as-needed -cc gcc -cclib -lz -cclib -lncurses -cclib '' compileFlags.cmx sadmanOutput.cmx all_sets.cmx alphSpec.cmx dequeue.cmx gz-0.5.7/gz.cmx ncursesML.cmx statusCommon.cmx status.cmx timer.cmx sexpr.cmx xml.cmx alphabet.cmx array_ops.cmx enum.cmx bitSet.cmx intSpec.cmx wordSpec.cmx specIndex.cmx characSpec.cmx character.cmx poyFile.cmx lz.cmx fileStream.cmx cost_matrix.cmx primes.cmx fingerPrint.cmx hennig.cmx hennigParser.cmx hennigLexer.cmx matrix.cmx methods.cmx nexus.cmx nexusParser.cmx nexusLexer.cmx sequence.cmx parser.cmx splitting.cmx data.cmx nonaddCS8.cmx addCS.cmx chromPam.cmx incList.cmx utl.cmx sufNode.cmx sufTree.cmx seed.cmx subseq.cmx block.cmx grappa/grappa.cmx utlGrappa.cmx genAli.cmx aliMap.cmx annchromAli.cmx annchrom.cmx annchromCS.cmx breakinvAli.cmx breakinv.cmx breakinvCS.cmx chromAli.cmx chrom.cmx chromCS.cmx genomeAli.cmx genome.cmx genomeCS.cmx seqCS.cmx dynamicCS.cmx memProfiler.cmx nonaddCS16.cmx nonaddCS32.cmx sankCS.cmx nodeSig.cmx node.cmx allDirNode.cmx asciiTree.cmx characterScripting.cmx edge.cmx tree.cmx ptree.cmx chartree.cmx allDirChar.cmx analyzer.cmx arguments.cmx camlpdf-0.3/glyphlist.cmx camlpdf-0.3/utility.cmx camlpdf-0.3/io.cmx camlpdf-0.3/transform.cmx camlpdf-0.3/pdf.cmx camlpdf-0.3/zlib.cmx camlpdf-0.3/pdfcodec.cmx camlpdf-0.3/pdfcrypt.cmx camlpdf-0.3/pdfwrite.cmx camlpdf-0.3/pdfread.cmx camlpdf-0.3/pdftext.cmx camlpdf-0.3/fonttables.cmx camlpdf-0.3/units.cmx camlpdf-0.3/paper.cmx camlpdf-0.3/pdfpages.cmx camlpdf-0.3/pdfdoc.cmx camlpdf-0.3/graphicpdf.cmx graphTree.cmx graphicsPs.cmx heap.cmx mst.cmx sampler.cmx queues.cmx sadman.cmx searchInformation.cmx sparceMatrix.cmx unionTree.cmx tabus.cmx treeSearch.cmx build.cmx buildNumber.cmx impliedAlignment.cmx charTransform.cmx commandLexer.cmx diagnosis.cmx rtree.cmx hash_tbl.cmx help.cmx helpIndex.cmx poyCommand.cmx poyFormaters.cmx poyParser.cmx supports.cmx version.cmx scripting.cmx phylo.cmx poy.cmx libgrappa.a libgzcaml.a libzlibstubs.a libpoycside.a -o poy.native
./libpoycside.a(ukkCommon.o): In function `copySequence':
/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukkCommon.c:92: undefined reference to `seq_get_len'
/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukkCommon.c:93: undefined reference to `seq_get_begin'
./libpoycside.a(ukk.checkp.o): In function `printTraceBack':
/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukk.checkp.c:489: undefined reference to `seq_prepend'
/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukk.checkp.c:490: undefined reference to `seq_prepend'
/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukk.checkp.c:491: undefined reference to `seq_prepend'
/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukk.checkp.c:493: undefined reference to `seq_prepend'
/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukk.checkp.c:494: undefined reference to `seq_prepend'
./libpoycside.a(ukk.checkp.o):/Data/clement/bin/old_poy/sources/poy4-release5-05-07/src/_build/ukk.checkp.c:495: more undefined references to `seq_prepend' follow

collect2: error: ld returned 1 exit status
File "caml_startup", line 1:
Error: Error during linking
Command exited with code 2.

Compilation unsuccessful after building 576 targets (0 cached) in 00:02:06.

Makefile:67: recipe for target 'poy.native' failed

make: *** [poy.native] Error 10

Clement Schneider

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Jul 21, 2016, 9:29:18 AM7/21/16

to POY - Phylogenetic Analysis Software

I was finally able to compile by switching to an older version of Ubuntu. I don't know what was the problem.

Ward C Wheeler

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Jul 21, 2016, 11:02:20 AM7/21/16

to po...@googlegroups.com

Glad it worked. Odd indeed.

W

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Nick Lucaroni

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Jul 22, 2016, 11:14:41 AM7/22/16

to POY Google Group

it's probably a gcc issue. we've experienced cmd line options being implicit that weren't in the past (--no-as-needed, for example).