installation issue involving the make command and syntax errors.

[Marco Mancuso]

Hello,

I was trying to get RAxML-NG on my Macbook Pro following the installation instructions of RAxML-NG at github:

https://github.com/amkozlov/raxml-ng.

I used this option: clone this repository and build RAxML-NG from scratch.

1- install the dependencies through homebrew (brew install flex

brew install bison
brew install gmp)

2- Build RAxML-NG.

PTHREADS version:

git clone --recursive https://github.com/amkozlov/raxml-ng
cd raxml-ng
mkdir build && cd build
cmake ..
make

When I run to the make command, this error is prompted: [  0%] [BISON][parse_utree_t] Building parser with bison 2.3

/path/to/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:168.9-19: syntax error, unexpected identifier, expecting string

make[2]: *** [libs/pll-modules/libs/libpll/src/parse_utree.c] Error 1

make[1]: *** [libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2

make: *** [all] Error 2.

I am not a programmer, hence I don't know how to fix this issue in the parse_utree.y file. Also, I noticed that, despite me having Bison updated to v.3.8.2., it still parses everything with a much older version (2.3.).

Any idea how to fix this? Thank you so much in advance for the help!

Best regards,

Marco.

[Oleksiy Kozlov]

Hi Marco,

please use pre-compiled M1 binary which works on all modern MacBooks (M1/M2/M3):

https://github.com/amkozlov/raxml-ng/releases/tag/1.2.1

Best,
Oleksiy

On 15.04.24 17:10, Marco Mancuso wrote:
> Hello,
> I was trying to get RAxML-NG on my Macbook Pro following the installation instructions of RAxML-NG
> at github:

> https://github.com/amkozlov/raxml-ng <https://github.com/amkozlov/raxml-ng>.

> I used this option: clone this repository and build RAxML-NG from scratch.
> 1- install the dependencies through homebrew (brew install flex
> brew install bison
> brew install gmp)

> *2- Build RAxML-NG.*
>
> PTHREADS version:
>
> git clone --recursive https://github.com/amkozlov/raxml-ng <https://github.com/amkozlov/raxml-ng>

> cd raxml-ng
> mkdir build && cd build
> cmake ..
> make
>

> When I run to the make command, this error is prompted: [  0%] *[BISON][parse_utree_t] Building
> parser with bison 2.3*

>
> /path/to/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:168.9-19: syntax error, unexpected
> identifier, expecting string
>
> make[2]: *** [libs/pll-modules/libs/libpll/src/parse_utree.c] Error 1
>
> make[1]: *** [libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2
>
> make: *** [all] Error 2.
>
> I am not a programmer, hence I don't know how to fix this issue in the parse_utree.y file. Also, I
> noticed that, despite me having Bison updated to v.3.8.2., it still parses everything with a much
> older version (2.3.).
>
> Any idea how to fix this? Thank you so much in advance for the help!
>
> Best regards,
>
> Marco.
>

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[Marco Mancuso]

Hello,

Unfortunately, my MacBook does not have a M1/M2/M3 processor as it older.

Would this version still work on my laptop?

Thanks for the speedy reply by the way!

Best regards,

Marco.

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[Oleksiy Kozlov]

I see, then x86_64 version should work for you:

https://github.com/amkozlov/raxml-ng/releases/download/1.2.1/raxml-ng_v1.2.1_macos_x86_64.zip

On 15.04.24 17:54, Marco Mancuso wrote:
> Hello,
> Unfortunately, my MacBook does not have a M1/M2/M3 processor as it older.
> Would this version still work on my laptop?
>
> Thanks for the speedy reply by the way!
>
> Best regards,
> Marco.
>
>

> Il lun 15 apr 2024, 17:41 Oleksiy Kozlov <alexei...@gmail.com <mailto:alexei...@gmail.com>>

> ha scritto:
>
> Hi Marco,
>
> please use pre-compiled M1 binary which works on all modern MacBooks (M1/M2/M3):
>
> https://github.com/amkozlov/raxml-ng/releases/tag/1.2.1
> <https://github.com/amkozlov/raxml-ng/releases/tag/1.2.1>
>
> Best,
> Oleksiy
>
> On 15.04.24 17:10, Marco Mancuso wrote:
> > Hello,
> > I was trying to get RAxML-NG on my Macbook Pro following the installation instructions of
> RAxML-NG
> > at github:
> > https://github.com/amkozlov/raxml-ng <https://github.com/amkozlov/raxml-ng>
> <https://github.com/amkozlov/raxml-ng <https://github.com/amkozlov/raxml-ng>>.
> > I used this option: clone this repository and build RAxML-NG from scratch.
> > 1- install the dependencies through homebrew (brew install flex
> > brew install bison
> > brew install gmp)
> > *2- Build RAxML-NG.*
> >
> > PTHREADS version:
> >
> > git clone --recursive https://github.com/amkozlov/raxml-ng

> <https://github.com/amkozlov/raxml-ng> <https://github.com/amkozlov/raxml-ng

> <https://github.com/amkozlov/raxml-ng>>
> > cd raxml-ng
> > mkdir build && cd build
> > cmake ..
> > make
> >
> > When I run to the make command, this error is prompted: [  0%] *[BISON][parse_utree_t] Building
> > parser with bison 2.3*
> >
> > /path/to/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:168.9-19: syntax error,
> unexpected
> > identifier, expecting string
> >
> > make[2]: *** [libs/pll-modules/libs/libpll/src/parse_utree.c] Error 1
> >
> > make[1]: *** [libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2
> >
> > make: *** [all] Error 2.
> >
> > I am not a programmer, hence I don't know how to fix this issue in the parse_utree.y file.
> Also, I
> > noticed that, despite me having Bison updated to v.3.8.2., it still parses everything with a
> much
> > older version (2.3.).
> >
> > Any idea how to fix this? Thank you so much in advance for the help!
> >
> > Best regards,
> >
> > Marco.
> >
> > --
> > You received this message because you are subscribed to the Google Groups "raxml" group.
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> >
> https://groups.google.com/d/msgid/raxml/9c8a598d-3931-47b5-b09d-0515f79d3dbbn%40googlegroups.com
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[Marco Mancuso]

Thank you so much! It works now :).

I managed to make this version work in the end: https://github.com/amkozlov/raxml-ng/releases/tag/1.2.1.

I know this might sound as a long stretch, but is it possible to know whether there is something like what you sent me for exaBayes too? I'm asking because I know the program is developed by your team as well.

I tried to install it some time ago but seems like the git clone command does not copy some necessary dependencies on my local environment.

Best regards,

Marco

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[Oleksiy Kozlov]

Hi Marco,

> Thank you so much! It works now :).
> I managed to make this version work in the end:
> https://github.com/amkozlov/raxml-ng/releases/tag/1.2.1

> <https://github.com/amkozlov/raxml-ng/releases/tag/1.2.1>.

Great!

> I know this might sound as a long stretch, but is it possible to know whether there is something
> like what you sent me for exaBayes too? I'm asking because I know the program is developed by your
> team as well.
> I tried to install it some time ago but seems like the git clone command does not copy some
> necessary dependencies on my local environment.

There seem to be pre-compiled binaries for older versions of ExaBayes, please see here:

https://cme.h-its.org/exelixis/web/software/exabayes/index.html

>
> Best regards,
> Marco
>
> Il giorno mar 16 apr 2024 alle ore 18:17 Oleksiy Kozlov <alexei...@gmail.com

> <mailto:alexei...@gmail.com>> ha scritto:

>
> I see, then x86_64 version should work for you:
>
> https://github.com/amkozlov/raxml-ng/releases/download/1.2.1/raxml-ng_v1.2.1_macos_x86_64.zip
> <https://github.com/amkozlov/raxml-ng/releases/download/1.2.1/raxml-ng_v1.2.1_macos_x86_64.zip>
>
> On 15.04.24 17:54, Marco Mancuso wrote:
> > Hello,
> > Unfortunately, my MacBook does not have a M1/M2/M3 processor as it older.
> > Would this version still work on my laptop?
> >
> > Thanks for the speedy reply by the way!
> >
> > Best regards,
> > Marco.
> >
> >
> > Il lun 15 apr 2024, 17:41 Oleksiy Kozlov <alexei...@gmail.com

> <mailto:alexei...@gmail.com> <mailto:alexei...@gmail.com <mailto:alexei...@gmail.com>>>

> <mailto:raxml%2Bunsu...@googlegroups.com <mailto:raxml%252Buns...@googlegroups.com>>
> >     <mailto:raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com <mailto:raxml%252Buns...@googlegroups.com>>>.

> >      > To view this discussion on the web visit
> >      >
> >
> https://groups.google.com/d/msgid/raxml/9c8a598d-3931-47b5-b09d-0515f79d3dbbn%40googlegroups.com
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> >      >
> >

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