Not compiling on Yosemite

[Leonardo Borges]

Dear all, 

I tried to compile pop 5.1.1 on a Yosemite Mac (10.5.5), but got some problems during make. I am not sure if it is related to the same problem mentioned on the previous topic (segmentation fault 1), so I have started a new topic.

I am running the latest xcode version (6.4) and ocaml 4.02.2 and I get the following error messages with "make":

make

ocamlbuild.native poy.native

Finished, 1 target (0 cached) in 00:00:00.

File "_tags", line 11, characters 88-96:

Warning: the tag "use_zlib" is not used in any flag or dependency declaration, so it will have no effect; it may be a typo. Otherwise you can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 12, characters 55-65:

Warning: the tag "use_parmap" is not used in any flag or dependency declaration, so it will have no effect; it may be a typo. Otherwise you can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

+ /opt/local/bin/ocamldep.opt -pp 'camlp4orf pa_extend.cmo' -modules poyExtension.ml > poyExtension.ml.depends

sh: camlp4orf: command not found

File "poyExtension.ml", line 1:

Error: Error while running external preprocessor

Command line: camlp4orf pa_extend.cmo 'poyExtension.ml' > /var/folders/jc/4c3zpsrn47b9l2px658wnkkr0000gn/T/ocamlppa11b00

Command exited with code 2.

Compilation unsuccessful after building 1 target (0 cached) in 00:00:00.

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

Just in case, this is the output of ./configure:

Ahoy-sexy:src Leo$ ./configure --enable-interface=flat

checking for gcc... gcc

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for hg... cat: ./VERSION: No such file or directory

no

checking whether we need to add --no-as-needed linking option... no

checking Whether to enable Concorde... no

checking SSE4 support... disabled

checking SSE3 support... disabled

checking for xslt-config... yes

checking how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/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... no

configure: WARNING: malloc.h: accepted by the compiler, rejected by the preprocessor!

configure: WARNING: malloc.h: proceeding with the compiler's result

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... no

checking for ocamlmktop... ocamlmktop

checking for OCaml version... 4.02.2

checking if OCaml supports dynamic linking in this architecture... yes

checking for ANSI C header files... (cached) yes

checking for fcntl.h... yes

checking for float.h... yes

checking for limits.h... 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 for sys/ioctl.h... 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 gcc 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... no

checking whether stat accepts an empty string... no

checking for library containing zlibVersion... -lz

checking for floor... yes

checking for gettimeofday... yes

checking for memset... yes

checking for pow... yes

checking for sqrt... yes

checking for sin... yes

checking for exp... yes

checking to enable likelihood... enabled

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1

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 poy.mltop

config.status: creating config.h

config.status: config.h is unchanged

Does anyone knows what may be happening?

Thanks for the help.

Leonardo

[Ward C Wheeler]

Leandro,

Here is a link to Yosemite “flat” interface binaries

https://www.dropbox.com/sh/u3kh7t2iftt6abd/AACkHYyO_GjC8h2G5mPjR26oa?dl=0

poy5.1.2 is sequential

poy5.1.2-mpi is parallel

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

[Nick Lucaroni]

The error is mentioning a missing camlp4orf, which is camlp4 a pretty printer and preprocessor that used to be installed with OCaml before <4.2 (now replaced with PPX).

Did you install OCaml with OPAM? In which case running

opam install camlp4

should resolve this issue.

--

nL

[Leonardo Borges]

Ward, thanks for the binaries. They are running!

Nick, I installed camlp4 with opam and (version 4.02+6), but I still get checking for camlp4orf... no 

Thanks,

Leonardo

[Nick Lucaroni]

Check the contents of your .opam directory for camlp4orf, and check if it's properly found on your path (you can run,  which camlp4orf ) . You may have to add the following to your .profile or .bashrc file to setup the environment for OCaml when you start the terminal,

. $HOME/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true
eval "`opam config env`"

Here are the contents of my .opam folder for the current release of OCaml after installing camlp4,

 

[φ] 14:40:22 ~/Repo/poy5 (master) $ ls -la /Users/nicholas.lucaroni/.opam/4.02.3/bin/
camlp4             camlp4of.opt       camlp4prof         mkcamlp4           ocamlc             ocamldep.opt       ocamllex.opt       ocamlopt.opt       ocamlyacc
camlp4boot         camlp4oof          camlp4r            ocaml              ocamlc.opt         ocamldoc           ocamlmklib         ocamloptp          safe_camlp4
camlp4o            camlp4oof.opt      camlp4r.opt        ocamlbuild         ocamlcp            ocamldoc.opt       ocamlmktop         ocamlprof
camlp4o.opt        camlp4orf          camlp4rf           ocamlbuild.byte    ocamldebug         ocamlfind          ocamlobjinfo       ocamlrun
camlp4of           camlp4orf.opt      camlp4rf.opt       ocamlbuild.native  ocamldep           ocamllex           ocamlopt           ocamlrun

--

nL

--

[Leonardo Borges]

Anyway, Just to let you know, Nick, I downloaded it again from github and still have the errors (I did not let it go through all the trouble):

Ahoy-sexy:src Leo$ ./configure --enable-interface=flat

checking for gcc... gcc

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for git... fatal: Not a git repository (or any of the parent directories): .git

checking for camlp4orf... camlp4orf

checking for ocamlmktop... ocamlmktop

checking for OCaml version... 4.02.0

Ahoy-sexy:src Leo$ make

ocamlbuild.native poy.native

Finished, 1 target (0 cached) in 00:00:00.

File "_tags", line 11, characters 88-96:

Warning: the tag "use_zlib" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 12, characters 55-65:

Warning: the tag "use_parmap" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 15, characters 163-177:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 17, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 18, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 19, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 20, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 21, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 22, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 23, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 24, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 25, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 26, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

00:00:02 4    (0   ) kolmoGrammar.cmo                                O-B----- |^Compilation unsuccessful after building 4 targets (0 cached) in 00:00:02.

Exception Sys.Break.

make: *** [poy.native] Error 100

aquitemcaqui.com

On 18 August 2015 at 23:19, Leonardo Borges <aquite...@gmail.com> wrote:

Now I remember. I dowloaded poy files from through the AMNH page.

Leo

aquitemcaqui.com

On 18 August 2015 at 23:18, Leonardo Borges <aquite...@gmail.com> wrote:

Hmmm. Maybe I do have the old version! I have being downloading and installing so many things these days and I don't remember anymore.

I will check it out!

Thank you!

Leo

aquitemcaqui.com

On 18 August 2015 at 23:05, Nick Lucaroni <nicholas....@gmail.com> wrote:

I thought I fixed that [0]. veclib is removed for Accelerate in OSX Yosemite [1].

Noticing a number of those deprecation warnings that I resolved, I'm pretty sure you're version might be slightly out of date. github will have the latest src release[2].

But feel free to stop here and use the binaries :-) .

--

nL

[0] : https://github.com/amnh/poy5/commit/28d843e99de757fc8f895869dbf35d3795e411fa

[1] : https://developer.apple.com/library/mac/documentation/MacOSX/Conceptual/OSX_Technology_Overview/SystemFrameworks/SystemFrameworks.html

[2] : https://github.com/amnh/poy5

On Tue, Aug 18, 2015 at 10:22 PM, Leonardo Borges <aquite...@gmail.com> wrote:

Nick, thanks for the tips.

I was able to fix camlp4 (I guess), since which camlp4 gives: /Users/Leo/.opam/4.02.0/bin/camlp4

Nonetheless, make did not work at all.

I am happy with Ward's binaries, but if you feel like going trough this, I am ok too. It will be interesting to try to solve that and maybe it is useful for someone else.

So, here is the horrible output of make:

Ahoy-sexy:src Leo$ make

ocamlbuild.native poy.native

Finished, 1 target (0 cached) in 00:00:01.

File "_tags", line 11, characters 88-96:

Warning: the tag "use_zlib" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 12, characters 55-65:

Warning: the tag "use_parmap" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 15, characters 163-177:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 17, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 18, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 19, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 20, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 21, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 22, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 23, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 24, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 25, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

File "_tags", line 26, characters 212-226:

Warning: the tag "use_extensions" is not used in any flag declaration, so it will have no effect; it may be a typo. Otherwise use `mark_tag_used` in your myocamlbuild.ml to disable this warning.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o statusCommon.cmo statusCommon.ml

File "statusCommon.ml", line 504, characters 21-33:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o fileStream.cmo fileStream.ml

File "fileStream.ml", line 48, characters 14-27:

Warning 3: deprecated: String.create

File "fileStream.ml", line 51, characters 21-31:

Warning 3: deprecated: String.set

File "fileStream.ml", line 59, characters 14-27:

Warning 3: deprecated: String.create

File "fileStream.ml", line 62, characters 21-31:

Warning 3: deprecated: String.set

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o allDirNode.cmo allDirNode.ml

File "allDirNode.ml", line 69, characters 22-40:

Warning 3: deprecated: Lazy.lazy_from_fun

File "allDirNode.ml", line 72, characters 14-32:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o sampler.cmo sampler.ml

File "sampler.ml", line 462, characters 22-34:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o allDirChar.cmo allDirChar.ml

File "allDirChar.ml", line 1415, characters 12-30:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o commandLexer.cmo commandLexer.ml

File "commandLexer.mll", line 104, characters 15-22:

Warning 3: deprecated: Format.bprintf

File "commandLexer.mll", line 437, characters 12-25:

Warning 3: deprecated: String.set

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -I gz-0.5.7 -I utils -I plugins -I ocamlmpi -I grappa -I camlpdf-0.3 -o gz-0.5.7/gz.cmx gz-0.5.7/gz.ml

File "gz-0.5.7/gz.ml", line 54, characters 15-28:

Warning 3: deprecated: String.create

File "gz-0.5.7/gz.ml", line 96, characters 12-25:

Warning 3: deprecated: String.create

File "gz-0.5.7/gz.ml", line 100, characters 18-31:

Warning 3: deprecated: String.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o statusCommon.cmx statusCommon.ml

File "statusCommon.ml", line 504, characters 21-33:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o numerical.cmx numerical.ml

File "numerical.ml", line 317, characters 24-43:

Warning 3: deprecated: Array.create_matrix

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o fileStream.cmx fileStream.ml

File "fileStream.ml", line 48, characters 14-27:

Warning 3: deprecated: String.create

File "fileStream.ml", line 51, characters 21-31:

Warning 3: deprecated: String.set

File "fileStream.ml", line 59, characters 14-27:

Warning 3: deprecated: String.create

File "fileStream.ml", line 62, characters 21-31:

Warning 3: deprecated: String.set

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o addGen.cmo addGen.ml

File "addGen.ml", line 105, characters 18-30:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o bitSet.cmx bitSet.ml

File "bitSet.ml", line 23, characters 40-53:

Warning 3: deprecated: String.create

File "bitSet.ml", line 28, characters 64-75:

Warning 3: deprecated: String.fill

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o cost_matrix.cmx cost_matrix.ml

File "cost_matrix.ml", line 1746, characters 8-26:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o mlModel.cmx mlModel.ml

File "mlModel.ml", line 675, characters 10-22:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I kolmo -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o kolmo/s_K.cmo kolmo/s_K.ml

File "kolmo/s_K.ml", line 87, characters 31-49:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -o camlpdf-0.3/utility.cmx camlpdf-0.3/utility.ml

File "camlpdf-0.3/utility.ml", line 177, characters 4-20:

Warning 3: deprecated: String.set

File "camlpdf-0.3/utility.ml", line 193, characters 15-28:

Warning 3: deprecated: String.create

File "camlpdf-0.3/utility.ml", line 196, characters 17-32:

Warning 3: deprecated: String.set

File "camlpdf-0.3/utility.ml", line 202, characters 10-23:

Warning 3: deprecated: String.create

File "camlpdf-0.3/utility.ml", line 203, characters 4-14:

Warning 3: deprecated: String.set

File "camlpdf-0.3/utility.ml", line 341, characters 16-29:

Warning 3: deprecated: String.create

File "camlpdf-0.3/utility.ml", line 343, characters 10-38:

Warning 3: deprecated: String.set

File "camlpdf-0.3/utility.ml", line 366, characters 14-27:

Warning 3: deprecated: String.create

File "camlpdf-0.3/utility.ml", line 368, characters 33-58:

Warning 3: deprecated: String.set

File "camlpdf-0.3/utility.ml", line 377, characters 6-42:

Warning 3: deprecated: String.set

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -o camlpdf-0.3/zlib.cmx camlpdf-0.3/zlib.ml

File "camlpdf-0.3/zlib.ml", line 34, characters 14-27:

Warning 3: deprecated: String.create

File "camlpdf-0.3/zlib.ml", line 35, characters 15-28:

Warning 3: deprecated: String.create

File "camlpdf-0.3/zlib.ml", line 58, characters 14-27:

Warning 3: deprecated: String.create

File "camlpdf-0.3/zlib.ml", line 59, characters 15-28:

Warning 3: deprecated: String.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -o camlpdf-0.3/pdfcodec.cmx camlpdf-0.3/pdfcodec.ml

File "camlpdf-0.3/pdfcodec.ml", line 224, characters 15-49:

Warning 3: deprecated: String.set

File "camlpdf-0.3/pdfcodec.ml", line 242, characters 19-45:

Warning 3: deprecated: String.set

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -o camlpdf-0.3/pdfcrypt.cmx camlpdf-0.3/pdfcrypt.ml

File "camlpdf-0.3/pdfcrypt.ml", line 200, characters 2-14:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -I camlpdf-0.3 -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -o camlpdf-0.3/pdftext.cmx camlpdf-0.3/pdftext.ml

File "camlpdf-0.3/pdftext.ml", line 902, characters 36-47:

Warning 3: deprecated: String.copy

File "camlpdf-0.3/pdftext.ml", line 903, characters 30-143:

Warning 3: deprecated: String.set

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -for-pack Kolmo -I kolmo -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o kolmo/s_K.cmx kolmo/s_K.ml

File "kolmo/s_K.ml", line 87, characters 31-49:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o genAli.cmx genAli.ml

File "genAli.ml", line 207, characters 35-44:

Warning 3: deprecated: Sort.list

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o addGen.cmx addGen.ml

File "addGen.ml", line 105, characters 18-30:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o breakinvAli.cmx breakinvAli.ml

File "breakinvAli.ml", line 573, characters 23-42:

Warning 3: deprecated: Array.create_matrix

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o block.cmx block.ml

File "block.ml", line 497, characters 20-32:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o genomeAli.cmx genomeAli.ml

File "genomeAli.ml", line 317, characters 23-35:

Warning 3: deprecated: Array.create

File "genomeAli.ml", line 318, characters 23-35:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o mlStaticCS.cmx mlStaticCS.ml

File "mlStaticCS.ml", line 441, characters 16-28:

Warning 3: deprecated: Array.create

File "mlStaticCS.ml", line 448, characters 42-54:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o node.cmx node.ml

File "node.ml", line 1892, characters 45-57:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o allDirNode.cmx allDirNode.ml

File "allDirNode.ml", line 69, characters 22-40:

Warning 3: deprecated: Lazy.lazy_from_fun

File "allDirNode.ml", line 72, characters 14-32:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o queues.cmo queues.ml

File "queues.ml", line 238, characters 45-63:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 328, characters 30-48:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 336, characters 30-48:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 346, characters 34-52:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 393, characters 25-43:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o sampler.cmx sampler.ml

File "sampler.ml", line 462, characters 22-34:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o sparceMatrix.cmx sparceMatrix.ml

File "sparceMatrix.ml", line 99, characters 23-41:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o queues.cmx queues.ml

File "queues.ml", line 238, characters 45-63:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 328, characters 30-48:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 336, characters 30-48:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 346, characters 34-52:

Warning 3: deprecated: Lazy.lazy_from_val

File "queues.ml", line 393, characters 25-43:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o treeSearch.cmx treeSearch.ml

File "treeSearch.ml", line 88, characters 4-22:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o modelSelection.cmx modelSelection.ml

File "modelSelection.ml", line 408, characters 18-30:

Warning 3: deprecated: Array.create

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o commandLexer.cmx commandLexer.ml

File "commandLexer.mll", line 104, characters 15-22:

Warning 3: deprecated: Format.bprintf

File "commandLexer.mll", line 437, characters 12-25:

Warning 3: deprecated: String.set

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o allDirChar.cmx allDirChar.ml

File "allDirChar.ml", line 1415, characters 12-30:

Warning 3: deprecated: Lazy.lazy_from_fun

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt -c -annot -bin-annot -I +camlp4 -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -bin-annot -pp 'camlp4orf kolmoGrammar.cmo kolmoExtension.cmo poyExtension.cmo  -DUSE_NATIVEDYNLINK  -DUSE_LIKELIHOOD           ' -I utils -I plugins -I ocamlmpi -I gz-0.5.7 -I grappa -I camlpdf-0.3 -o scripting.cmx scripting.ml

File "scripting.ml", line 4831, characters 17-35:

Warning 3: deprecated: Lazy.lazy_from_val

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/mgr_graph_components.c

grappa/mgr_graph_components.c:613:24: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]

        (components[i].blocks == 1)) {

         ~~~~~~~~~~~~~~~~~~~~~^~~~

grappa/mgr_graph_components.c:613:24: note: remove extraneous parentheses around the comparison to silence this warning

        (components[i].blocks == 1)) {

        ~                     ^   ~

grappa/mgr_graph_components.c:613:24: note: use '=' to turn this equality comparison into an assignment

        (components[i].blocks == 1)) {

                              ^~

                              =

1 warning generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/mgr_uniinvdist.c

grappa/mgr_uniinvdist.c:283:10: warning: implicit declaration of function 'invdist_noncircular' is invalid in C99 [-Wimplicit-function-declaration]

  dist = invdist_noncircular(g1, g2, offset, num_genes, &distmem);

         ^

1 warning generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/mgr_genome_ops.c

grappa/mgr_genome_ops.c:506:31: warning: implicit declaration of function 'mcdist_noncircular' is invalid in C99 [-Wimplicit-function-declaration]

                                dist_mat[i*nb_spec + j] = mcdist_noncircular(&genome_list[i], &genome_list[j], 

                                                          ^

1 warning generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/mgr_list_ops.c

grappa/mgr_list_ops.c:360:16: warning: implicit declaration of function 'mcdist_noncircular' is invalid in C99 [-Wimplicit-function-declaration]

                  edge_dif = mcdist_noncircular(&genome_list[the_edge_list->label1],

                             ^

1 warning generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/mgr.c

grappa/mgr.c:1247:26: warning: unsequenced modification and access to 'tmplist' [-Wunsequenced]

        (tmplist, tmplist++, num_genes, num_chromosomes, dist_mem_cap,NULL);

         ~~~~~~~         ^

grappa/mgr.c:1246:9: warning: unused variable 'dis' [-Wunused-variable]

    int dis = mcdist_capgraph 

        ^

2 warnings generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/vertex_factory.c

grappa/vertex_factory.c:183:20: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]

    if (( vf->head == NULL ))

          ~~~~~~~~~^~~~~~~

grappa/vertex_factory.c:183:20: note: remove extraneous parentheses around the comparison to silence this warning

    if (( vf->head == NULL ))

        ~          ^       ~

grappa/vertex_factory.c:183:20: note: use '=' to turn this equality comparison into an assignment

    if (( vf->head == NULL ))

                   ^~

                   =

1 warning generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/sorting_reversal_median.c

grappa/sorting_reversal_median.c:125:9: warning: implicit declaration of function 'mark_vertex' is invalid in C99 [-Wimplicit-function-declaration]

        mark_vertex (mm->vf,vorig);

        ^

grappa/sorting_reversal_median.c:318:91: warning: multi-line // comment [-Wcomment]

                   // fprintf(stdout,"n->worst possible is better than any median so far, \

                                                                                          ^

grappa/sorting_reversal_median.c:319:84: warning: multi-line // comment [-Wcomment]

                            copy from n->perm to median->genes, set MAX_MED to %d\n\

                                                                                   ^

3 warnings generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c grappa/grappa_interface.c

grappa/grappa_interface.c:327:5: warning: implicit declaration of function 'better_capping' is invalid in C99 [-Wimplicit-function-declaration]

    better_capping (g1->genes,g2->genes,NUM_GENES,g1->delimiters,g2->delimiters,g1->deli_num,g2->deli_num,out_genome_list);

    ^

grappa/grappa_interface.c:405:9: warning: implicit declaration of function 'free_mem_4_mgr' is invalid in C99 [-Wimplicit-function-declaration]

        free_mem_4_mgr();

        ^

grappa/grappa_interface.c:476:17: warning: implicit declaration of function 'coalestsp' is invalid in C99 [-Wimplicit-function-declaration]

                coalestsp ( 2 * num_cond, cond3mem_p->con_med->genes,FALSE, 

                ^

3 warnings generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c algn.c

algn.c:1047:20: warning: comparison of constant 1000000 with expression of type 'unsigned short' is always false [-Wtautological-constant-out-of-range-compare]

        if (arr[i] >= HIGH_NUM) printf ("INF ");

            ~~~~~~ ^  ~~~~~~~~

1 warning generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlc.opt -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ -ccopt -DUSE_NATIVEDYNLINK -ccopt -DUSE_LIKELIHOOD -cc gcc -ccopt -Wall -ccopt -I -ccopt //usr/include/malloc -ccopt -isysroot -ccopt / -ccopt -g -ccopt -O2 -c gamma.c

gamma.c:75:29: warning: 'gamma' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]

    v_g = caml_copy_double( gamma( Double_val( v_x ) ) );

                            ^

gamma.c:52:8: note: 'gamma' has been explicitly marked deprecated here

double gamma( double z )

       ^

gamma.c:133:59: warning: 'gamma' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]

    return (pow(beta,alpha)*pow(r, alpha-1))/(exp(beta*r)*gamma(alpha));

                                                          ^

gamma.c:52:8: note: 'gamma' has been explicitly marked deprecated here

double gamma( double z )

       ^

2 warnings generated.

+ /Users/Leo/.opam/4.02.0/bin/ocamlmklib -o grappa -cclib -framework -cclib veclib -cclib -lz -cclib -isysroot -cclib / -cclib -lm -cclib '' -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ grappa/uf.o grappa/bbtsp.o grappa/bitvector.o grappa/invdist.o grappa/cheaptsp.o grappa/correction.o grappa/condense3.o grappa/convert.o grappa/binencode.o grappa/lists.o grappa/lk_main.o grappa/med_util.o grappa/mgr_check.o grappa/mgr_e_malloc.o grappa/mgr_graph_edit.o grappa/mgr_mcread_input.o grappa/mgr_genome_print.o grappa/mgr_write_data.o grappa/mgr_scenario.o grappa/mgr_graph_components.o grappa/mgr_mcrdist.o grappa/mgr_uniinvdist.o grappa/mgr_genome_ops.o grappa/mgr_list_ops.o grappa/mgr_my_testrev.o grappa/mgr.o grappa/all_sorting_reversals.o grappa/vertex_factory.o grappa/hashtable.o grappa/priority_stack.o grappa/sorting_reversal_median.o grappa/inversion_median.o grappa/inversion_median_alberto.o grappa/grappa_interface.o

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libgrappa.a(lk_main.o) has no symbols

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libgrappa.a(lk_main.o) has no symbols

+ /Users/Leo/.opam/4.02.0/bin/ocamlmklib -o poycside -cclib -framework -cclib veclib -cclib -lz -cclib -isysroot -cclib / -cclib -lm -cclib '' -ccopt -I -ccopt //usr/include/malloc -ccopt -I -ccopt //usr/include/ add.o algn.o avl.o floatmatrix.o fm.o falgn.o gamma.o getrusage.o likelihood.o memstack.o mlxslt.o newkkonen.o ncurses.o nonaddCSc8.o nonaddCSc16.o nonaddCSc32.o queue_with_linkedlist.o readlineml.o sankoff.o sleep.o ukk.checkp.o ukkCommon.o zarr.o

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libpoycside.a(mlxslt.o) has no symbols

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libpoycside.a(ncurses.o) has no symbols

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libpoycside.a(readlineml.o) has no symbols

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libpoycside.a(mlxslt.o) has no symbols

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libpoycside.a(ncurses.o) has no symbols

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ./libpoycside.a(readlineml.o) has no symbols

+ /Users/Leo/.opam/4.02.0/bin/ocamlopt.opt dynlink.cmxa unix.cmxa str.cmxa bigarray.cmxa -I +camlp4 camlp4fulllib.cmxa -cclib -lpoycside -cclib -L. -ccopt -I -ccopt //usr/lib -cclib -lgrappa -cclib -L. -cc gcc -cclib -framework -cclib veclib -cclib -lz -cclib -isysroot -cclib / -cclib -lm -cclib '' addGen.cmx addVec.cmx compileFlags.cmx sadmanOutput.cmx all_sets.cmx enum.cmx bitSet.cmx gz-0.5.7/gz.cmx poyFile.cmx lz.cmx statusCommon.cmx fileStream.cmx timer.cmx status.cmx numerical.cmx sexpr.cmx methods.cmx utl.cmx cost_matrix.cmx xml.cmx alphabet.cmx array_ops.cmx binaryTree.cmx block_mauve_seed.cmx primes.cmx fingerPrint.cmx matrix.cmx sequence.cmx block_mauve_mum.cmx block_mauve_lcb.cmx block_mauve.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 dyn_pam.cmx fMatrix.cmx fileContents.cmx fasta.cmx mlModel.cmx floatSequence.cmx grappa/grappa.cmx utlGrappa.cmx genAli.cmx tree.cmx nexus.cmx parser.cmx hennig.cmx heap.cmx kolmo.cmx phylip.cmx splitting.cmx data.cmx nonaddCS8.cmx addCS.cmx chromPam.cmx incList.cmx sufNode.cmx sufTree.cmx seed.cmx subseq.cmx block.cmx aliMap.cmx annchromAli.cmx annchrom.cmx annchromCS.cmx breakinvAli.cmx breakinv.cmx breakinvCS.cmx chromAli.cmx chrom.cmx chromCS.cmx genNonAdd.cmx genomeAli.cmx genome.cmx genomeCS.cmx mlStaticCS.cmx seqCS.cmx mlDynamicCS.cmx dynamicCS.cmx sankCS.cmx fixed_states.cmx kolmoCS.cmx memProfiler.cmx nonaddCS16.cmx nonaddCS32.cmx nodeSig.cmx node.cmx allDirNode.cmx asciiTree.cmx edge.cmx ptree.cmx chartree.cmx impliedAlignment.cmx allDirChar.cmx analyzer.cmx arguments.cmx graphTree.cmx graphicsPs.cmx mst.cmx sampler.cmx queues.cmx sadman.cmx searchInformation.cmx sparceMatrix.cmx unionTree.cmx tabus.cmx treeSearch.cmx build.cmx buildNumber.cmx modelSelection.cmx charTransform.cmx commandLexer.cmx compOut.cmx diagnosis.cmx help.cmx helpIndex.cmx mlTestStat.cmx poyCommand.cmx poyFormaters.cmx supports.cmx version.cmx scripting.cmx phylo.cmx poy.cmx libgrappa.a libgzcaml.a libzlibstubs.a libpoycside.a -o poy.native

ld: framework not found veclib

clang: error: linker command failed with exit code 1 (use -v to see invocation)

File "caml_startup", line 1:

Error: Error during linking

Command exited with code 2.

Compilation unsuccessful after building 769 targets (0 cached) in 00:08:46.

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

Cheers,

Leo

aquitemcaqui.com

[Nick Lucaroni]

Those warnings are all fine. It looks like you cancelled early after seeing them?

...