Error In Installing FreeBayes

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Error In Installing FreeBayes

Dr Priyanka Jain

Dear Sir/Madam,
                    
  I am trying to clone freebayes from following link :

To download freebayes, please use git to download the most recent development tr

    git clone --recursive git://github.com/ekg/freebayes.git


## Compilationfreebayes requires g++, camke, the standard C and C++ development libraries, lib
To build, users can just run:

    make -j4

Error i am getting is 

- Found LibLZMA: /home/sb-102/anaconda3/lib/liblzma.so (found version "5.2.4")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_kill
-- Looking for pthread_kill - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /home/NFS/37_hg/freebayes/build
/usr/bin/gmake: unrecognized option '--jobserver-auth=3,4'
Usage: gmake [options] [target] ...
Options:
  -b, -m                      Ignored for compatibility.
  -B, --always-make           Unconditionally make all targets.
  -C DIRECTORY, --directory=DIRECTORY
                              Change to DIRECTORY before doing anything.
  -d                          Print lots of debugging information.
  --debug[=FLAGS]             Print various types of debugging information.
  -e, --environment-overrides
                              Environment variables override makefiles.
  --eval=STRING               Evaluate STRING as a makefile statement.
  -f FILE, --file=FILE, --makefile=FILE
                              Read FILE as a makefile.
  -h, --help                  Print this message and exit.
  -i, --ignore-errors         Ignore errors from recipes.
  -I DIRECTORY, --include-dir=DIRECTORY
                              Search DIRECTORY for included makefiles.
  -j [N], --jobs[=N]          Allow N jobs at once; infinite jobs with no arg.
  -k, --keep-going            Keep going when some targets can't be made.
  -l [N], --load-average[=N], --max-load[=N]
                              Don't start multiple jobs unless load is below N.
  -L, --check-symlink-times   Use the latest mtime between symlinks and target.
  -n, --just-print, --dry-run, --recon
                              Don't actually run any recipe; just print them.
  -o FILE, --old-file=FILE, --assume-old=FILE
                              Consider FILE to be very old and don't remake it.
  -p, --print-data-base       Print make's internal database.
  -q, --question              Run no recipe; exit status says if up to date.
  -r, --no-builtin-rules      Disable the built-in implicit rules.
  -R, --no-builtin-variables  Disable the built-in variable settings.
  -s, --silent, --quiet       Don't echo recipes.
  -S, --no-keep-going, --stop
                              Turns off -k.
  -t, --touch                 Touch targets instead of remaking them.
  -v, --version               Print the version number of make and exit.
  -w, --print-directory       Print the current directory.
  --no-print-directory        Turn off -w, even if it was turned on implicitly.
  -W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE
                              Consider FILE to be infinitely new.
  --warn-undefined-variables  Warn when an undefined variable is referenced.
  --warn-undefined-functions  Warn when an undefined user function is called.

This program built for x86_64-redhat-linux-gnu
Report bugs to <[hidden email]>
make: *** [Makefile:6: freebayes] Error 2

Kindly help me to resolve this error

With Regards,
Dr Priyanka Jain (PhD),
Mobile : 9718854136
Researcher,National Research Centre on Plant Biotechnology,
LBS Centre, Pusa Campus, New Delhi – 110012, INDIA






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Re: Error In Installing FreeBayes

Henrik Carlqvist
On Fri, 6 Mar 2020 09:38:19 +0530
Dr Priyanka Jain <[hidden email]> wrote:
>   I am trying to clone freebayes from following link :

> /usr/bin/gmake: unrecognized option '--jobserver-auth=3,4'

It seems as if your project "freebayes" requires a newer version of gnu
make than you have installed. You can check which version of gnu make you
have with:

gmake --version

Example of output:

gmake --version
GNU Make 4.1
Built for x86_64-slackware-linux-gnu
Copyright (C) 1988-2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html> This is free software: you are free to
change and redistribute it. There is NO WARRANTY, to the extent permitted
by law.

In the above example I have Gnu Make version 4.1.

According to
https://lists.gnu.org/archive/html/info-gnu/2016-05/msg00013.html it
seems as if the --jobserver-auth option was introduced with version 4.2 of
Gnu Make.

So you will need to update your installed version of Gnu Make or adjust
the build scripts to comply with your older version.

regards Henrik

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Re: Error In Installing FreeBayes

Martin Dorey-2
> adjust the build scripts to comply with your older version

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=827132 (debhelper: make-4.2 renamed --jobserver-fds to --jobserver-auth causing parallel build issues) shows it’s not impossible that third party build scripts might hard code such details of GNU Make’s implementation but I doubt that’s what’s happening here.  Didn’t we have a report, which, away from my desk, I can’t find, from some user who turned out to have two installations of make, and a situation where a new (jobserver-auth) make ended up running an old (jobserver-fds) one, failing with this kind of symptom?


From: Bug-make <bug-make-bounces+martin.dorey=[hidden email]> on behalf of Henrik Carlqvist <[hidden email]>
Sent: Thursday, March 5, 2020 22:50
To: Dr Priyanka Jain
Cc: [hidden email]
Subject: Re: Error In Installing FreeBayes
 
***** EXTERNAL EMAIL *****

On Fri, 6 Mar 2020 09:38:19 +0530
Dr Priyanka Jain <[hidden email]> wrote:
>   I am trying to clone freebayes from following link :

> /usr/bin/gmake: unrecognized option '--jobserver-auth=3,4'

It seems as if your project "freebayes" requires a newer version of gnu
make than you have installed. You can check which version of gnu make you
have with:

gmake --version

Example of output:

gmake --version
GNU Make 4.1
Built for x86_64-slackware-linux-gnu
Copyright (C) 1988-2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgnu.org%2Flicenses%2Fgpl.html&amp;data=01%7C01%7CMartin.Dorey%40hitachivantara.com%7Cfb8a9d366f6840cbfddb08d7c19aa86a%7C18791e1761594f52a8d4de814ca8284a%7C0&amp;sdata=KOr6%2B28yX8rw7KEzpFQUR8CUfPy0iI7zAaUzUo331yk%3D&amp;reserved=0> This is free software: you are free to
change and redistribute it. There is NO WARRANTY, to the extent permitted
by law.

In the above example I have Gnu Make version 4.1.

According to
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.gnu.org%2Farchive%2Fhtml%2Finfo-gnu%2F2016-05%2Fmsg00013.html&amp;data=01%7C01%7CMartin.Dorey%40hitachivantara.com%7Cfb8a9d366f6840cbfddb08d7c19aa86a%7C18791e1761594f52a8d4de814ca8284a%7C0&amp;sdata=iOpF3v%2BvGDz3lpepSahoVG6glcl6b1yV90qHxS8SaZc%3D&amp;reserved=0 it
seems as if the --jobserver-auth option was introduced with version 4.2 of
Gnu Make.

So you will need to update your installed version of Gnu Make or adjust
the build scripts to comply with your older version.

regards Henrik

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Re: Error In Installing FreeBayes

Paul Smith-20
In reply to this post by Dr Priyanka Jain
On Fri, 2020-03-06 at 09:38 +0530, Dr Priyanka Jain wrote:
> -- Build files have been written to: /home/NFS/37_hg/freebayes/build
> /usr/bin/gmake: unrecognized option '--jobserver-auth=3,4'

This means that the version of make being invoked as a sub-make is
different from the version of make you invoked from the command line.

This is why all makefiles should always use '$(MAKE)' when invoking
submakes and never hardcode a name like 'make' directly.  The '$(MAKE)'
variable should always contain the currently-running instance of make.

You can see that you are running 'make -j4' but somehow the build
system is trying to invoke '/usr/bin/gmake' which is a different
version of make.

I can't explain why that would happen; I think makefiles generated by
cmake are usually written correctly.  Maybe there's a bug in cmake or
maybe the cmake files you're using are trying to directly invoke make
somehow.

The simplest solution is for you to run the same version of make that
cmake wants, which in this case appears to be '/usr/bin/gmake'.