From j.abbott at imperial.ac.uk  Wed Dec  8 07:05:58 2010
From: j.abbott at imperial.ac.uk (James Abbott)
Date: Wed, 8 Dec 2010 12:05:58 +0000
Subject: [emboss-dev] CVS checkout generates broken configure script...
Message-ID: <20101208120558.GB2915@pseudogene>

Hello,

I'm trying to build a clean CVS checkout of the emboss code, but the
configure script generated by autoconf contains a syntax error:

checking for HPDF_New in -lhpdf... yes
PDF support found
checking whether to look for gsoap support... no
checking whether to look for axis2c support... ./configure: line 13496:
syntax error near unexpected token `AXIS2C,axis2c,'
./configure: line 13496: `    PKG_CHECK_MODULES(AXIS2C,axis2c,'


The relevent section of configure looks like:

======================================================================
if test "x$with_axis2c" != xno; then :

    { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
    if test "x$with_axis2c" != "xyes" ; then
        ALT_HOME=$with_axis2c
        if test ! -d "${ALT_HOME}" ; then
          as_fn_error $? "No such axis2c directory (${ALT_HOME})"
"$LINENO" 5
        fi
         export
PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$ALT_HOME/lib/pkgconfig"
    else  
        ALT_HOME="/usr"
    fi    

    PKG_CHECK_MODULES(AXIS2C,axis2c,

        AXIS2C_CPPFLAGS=${AXIS2C_CFLAGS}
        AXIS2C_LDFLAGS=${AXIS2C_LIBS}
    ,

        echo pkg-config axis2c detection failed
    )

======================================================================

I'm using the following versions on a CentOS5.5 machine:

autoconf (GNU Autoconf) 2.68
ltmain.sh (GNU libtool) 2.2
automake (GNU automake) 1.9.6

and after checking out the code ran:

autoreconf -fiv
./configure --enable-warnings --disable-shared --enable-debug

Does anyone have any idea if the current CVS version is sick, or if this
is a problem with my environment/versions etc.?

Best Regards,
James
-- 
Dr. James Abbott
Bioinformatics Software Developer
Imperial College, London

From ajb at ebi.ac.uk  Wed Dec  8 07:45:55 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 8 Dec 2010 12:45:55 -0000 (UTC)
Subject: [emboss-dev] CVS checkout generates broken configure script...
In-Reply-To: <20101208120558.GB2915@pseudogene>
References: <20101208120558.GB2915@pseudogene>
Message-ID: <39822.86.26.12.63.1291812355.squirrel@webmail.ebi.ac.uk>

Hello James,

There is currently a dependency on pkgconfig in CVS. You are missing
the pkg.m4 file on your system. In CentOS you can probably get it by
installing the pkgconfig RPM (which I can see exists for CentOS
using a google search).

I'll have a look at this after I return from holiday in the new year.

HTH

Alan


> Hello,
>
> I'm trying to build a clean CVS checkout of the emboss code, but the
> configure script generated by autoconf contains a syntax error:
>
> checking for HPDF_New in -lhpdf... yes
> PDF support found
> checking whether to look for gsoap support... no
> checking whether to look for axis2c support... ./configure: line 13496:
> syntax error near unexpected token `AXIS2C,axis2c,'
> ./configure: line 13496: `    PKG_CHECK_MODULES(AXIS2C,axis2c,'
>
>
> The relevent section of configure looks like:
>
> ======================================================================
> if test "x$with_axis2c" != xno; then :
>
>     { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
> $as_echo "yes" >&6; }
>     if test "x$with_axis2c" != "xyes" ; then
>         ALT_HOME=$with_axis2c
>         if test ! -d "${ALT_HOME}" ; then
>           as_fn_error $? "No such axis2c directory (${ALT_HOME})"
> "$LINENO" 5
>         fi
>          export
> PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$ALT_HOME/lib/pkgconfig"
>     else
>         ALT_HOME="/usr"
>     fi
>
>     PKG_CHECK_MODULES(AXIS2C,axis2c,
>
>         AXIS2C_CPPFLAGS=${AXIS2C_CFLAGS}
>         AXIS2C_LDFLAGS=${AXIS2C_LIBS}
>     ,
>
>         echo pkg-config axis2c detection failed
>     )
>
> ======================================================================
>
> I'm using the following versions on a CentOS5.5 machine:
>
> autoconf (GNU Autoconf) 2.68
> ltmain.sh (GNU libtool) 2.2
> automake (GNU automake) 1.9.6
>
> and after checking out the code ran:
>
> autoreconf -fiv
> ./configure --enable-warnings --disable-shared --enable-debug
>
> Does anyone have any idea if the current CVS version is sick, or if this
> is a problem with my environment/versions etc.?
>
> Best Regards,
> James
> --
> Dr. James Abbott
> Bioinformatics Software Developer
> Imperial College, London
> _______________________________________________
> emboss-dev mailing list
> emboss-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss-dev
>



From j.abbott at imperial.ac.uk  Wed Dec  8 08:00:09 2010
From: j.abbott at imperial.ac.uk (James Abbott)
Date: Wed, 8 Dec 2010 13:00:09 +0000
Subject: [emboss-dev] CVS checkout generates broken configure script...
In-Reply-To: <39822.86.26.12.63.1291812355.squirrel@webmail.ebi.ac.uk>
References: <20101208120558.GB2915@pseudogene>
	<39822.86.26.12.63.1291812355.squirrel@webmail.ebi.ac.uk>
Message-ID: <20101208130009.GC2915@pseudogene>

Hi Alan,

That was indeed the problem - pkgconfig was installed, but my
autoconf/automake/libtool installations are in a non-standard location
so as not to interfere with the OS packaged versions. These use a
different share/aclocal directory, which did not contain pgk.m4....

Many thanks,
James
 
On Wed, Dec 08, 2010 at 12:45:55PM +0000, ajb at ebi.ac.uk wrote:
> Hello James,
> 
> There is currently a dependency on pkgconfig in CVS. You are missing
> the pkg.m4 file on your system. In CentOS you can probably get it by
> installing the pkgconfig RPM (which I can see exists for CentOS
> using a google search).
> 
> I'll have a look at this after I return from holiday in the new year.
> 
> HTH
> 
> Alan
> 
> 
> > Hello,
> >
> > I'm trying to build a clean CVS checkout of the emboss code, but the
> > configure script generated by autoconf contains a syntax error:
> >
> > checking for HPDF_New in -lhpdf... yes
> > PDF support found
> > checking whether to look for gsoap support... no
> > checking whether to look for axis2c support... ./configure: line 13496:
> > syntax error near unexpected token `AXIS2C,axis2c,'
> > ./configure: line 13496: `    PKG_CHECK_MODULES(AXIS2C,axis2c,'
> >
> >
> > The relevent section of configure looks like:
> >
> > ======================================================================
> > if test "x$with_axis2c" != xno; then :
> >
> >     { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
> > $as_echo "yes" >&6; }
> >     if test "x$with_axis2c" != "xyes" ; then
> >         ALT_HOME=$with_axis2c
> >         if test ! -d "${ALT_HOME}" ; then
> >           as_fn_error $? "No such axis2c directory (${ALT_HOME})"
> > "$LINENO" 5
> >         fi
> >          export
> > PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$ALT_HOME/lib/pkgconfig"
> >     else
> >         ALT_HOME="/usr"
> >     fi
> >
> >     PKG_CHECK_MODULES(AXIS2C,axis2c,
> >
> >         AXIS2C_CPPFLAGS=${AXIS2C_CFLAGS}
> >         AXIS2C_LDFLAGS=${AXIS2C_LIBS}
> >     ,
> >
> >         echo pkg-config axis2c detection failed
> >     )
> >
> > ======================================================================
> >
> > I'm using the following versions on a CentOS5.5 machine:
> >
> > autoconf (GNU Autoconf) 2.68
> > ltmain.sh (GNU libtool) 2.2
> > automake (GNU automake) 1.9.6
> >
> > and after checking out the code ran:
> >
> > autoreconf -fiv
> > ./configure --enable-warnings --disable-shared --enable-debug
> >
> > Does anyone have any idea if the current CVS version is sick, or if this
> > is a problem with my environment/versions etc.?
> >
> > Best Regards,
> > James
> > --
> > Dr. James Abbott
> > Bioinformatics Software Developer
> > Imperial College, London
> > _______________________________________________
> > emboss-dev mailing list
> > emboss-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss-dev
> >
> 
> 

-- 
Dr. James Abbott
Bioinformatics Software Developer
Imperial College, London

From j.abbott at imperial.ac.uk  Wed Dec  8 12:05:58 2010
From: j.abbott at imperial.ac.uk (James Abbott)
Date: Wed, 8 Dec 2010 12:05:58 +0000
Subject: [emboss-dev] CVS checkout generates broken configure script...
Message-ID: <20101208120558.GB2915@pseudogene>

Hello,

I'm trying to build a clean CVS checkout of the emboss code, but the
configure script generated by autoconf contains a syntax error:

checking for HPDF_New in -lhpdf... yes
PDF support found
checking whether to look for gsoap support... no
checking whether to look for axis2c support... ./configure: line 13496:
syntax error near unexpected token `AXIS2C,axis2c,'
./configure: line 13496: `    PKG_CHECK_MODULES(AXIS2C,axis2c,'


The relevent section of configure looks like:

======================================================================
if test "x$with_axis2c" != xno; then :

    { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
    if test "x$with_axis2c" != "xyes" ; then
        ALT_HOME=$with_axis2c
        if test ! -d "${ALT_HOME}" ; then
          as_fn_error $? "No such axis2c directory (${ALT_HOME})"
"$LINENO" 5
        fi
         export
PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$ALT_HOME/lib/pkgconfig"
    else  
        ALT_HOME="/usr"
    fi    

    PKG_CHECK_MODULES(AXIS2C,axis2c,

        AXIS2C_CPPFLAGS=${AXIS2C_CFLAGS}
        AXIS2C_LDFLAGS=${AXIS2C_LIBS}
    ,

        echo pkg-config axis2c detection failed
    )

======================================================================

I'm using the following versions on a CentOS5.5 machine:

autoconf (GNU Autoconf) 2.68
ltmain.sh (GNU libtool) 2.2
automake (GNU automake) 1.9.6

and after checking out the code ran:

autoreconf -fiv
./configure --enable-warnings --disable-shared --enable-debug

Does anyone have any idea if the current CVS version is sick, or if this
is a problem with my environment/versions etc.?

Best Regards,
James
-- 
Dr. James Abbott
Bioinformatics Software Developer
Imperial College, London


From ajb at ebi.ac.uk  Wed Dec  8 12:45:55 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 8 Dec 2010 12:45:55 -0000 (UTC)
Subject: [emboss-dev] CVS checkout generates broken configure script...
In-Reply-To: <20101208120558.GB2915@pseudogene>
References: <20101208120558.GB2915@pseudogene>
Message-ID: <39822.86.26.12.63.1291812355.squirrel@webmail.ebi.ac.uk>

Hello James,

There is currently a dependency on pkgconfig in CVS. You are missing
the pkg.m4 file on your system. In CentOS you can probably get it by
installing the pkgconfig RPM (which I can see exists for CentOS
using a google search).

I'll have a look at this after I return from holiday in the new year.

HTH

Alan


> Hello,
>
> I'm trying to build a clean CVS checkout of the emboss code, but the
> configure script generated by autoconf contains a syntax error:
>
> checking for HPDF_New in -lhpdf... yes
> PDF support found
> checking whether to look for gsoap support... no
> checking whether to look for axis2c support... ./configure: line 13496:
> syntax error near unexpected token `AXIS2C,axis2c,'
> ./configure: line 13496: `    PKG_CHECK_MODULES(AXIS2C,axis2c,'
>
>
> The relevent section of configure looks like:
>
> ======================================================================
> if test "x$with_axis2c" != xno; then :
>
>     { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
> $as_echo "yes" >&6; }
>     if test "x$with_axis2c" != "xyes" ; then
>         ALT_HOME=$with_axis2c
>         if test ! -d "${ALT_HOME}" ; then
>           as_fn_error $? "No such axis2c directory (${ALT_HOME})"
> "$LINENO" 5
>         fi
>          export
> PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$ALT_HOME/lib/pkgconfig"
>     else
>         ALT_HOME="/usr"
>     fi
>
>     PKG_CHECK_MODULES(AXIS2C,axis2c,
>
>         AXIS2C_CPPFLAGS=${AXIS2C_CFLAGS}
>         AXIS2C_LDFLAGS=${AXIS2C_LIBS}
>     ,
>
>         echo pkg-config axis2c detection failed
>     )
>
> ======================================================================
>
> I'm using the following versions on a CentOS5.5 machine:
>
> autoconf (GNU Autoconf) 2.68
> ltmain.sh (GNU libtool) 2.2
> automake (GNU automake) 1.9.6
>
> and after checking out the code ran:
>
> autoreconf -fiv
> ./configure --enable-warnings --disable-shared --enable-debug
>
> Does anyone have any idea if the current CVS version is sick, or if this
> is a problem with my environment/versions etc.?
>
> Best Regards,
> James
> --
> Dr. James Abbott
> Bioinformatics Software Developer
> Imperial College, London
> _______________________________________________
> emboss-dev mailing list
> emboss-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss-dev
>




From j.abbott at imperial.ac.uk  Wed Dec  8 13:00:09 2010
From: j.abbott at imperial.ac.uk (James Abbott)
Date: Wed, 8 Dec 2010 13:00:09 +0000
Subject: [emboss-dev] CVS checkout generates broken configure script...
In-Reply-To: <39822.86.26.12.63.1291812355.squirrel@webmail.ebi.ac.uk>
References: <20101208120558.GB2915@pseudogene>
	<39822.86.26.12.63.1291812355.squirrel@webmail.ebi.ac.uk>
Message-ID: <20101208130009.GC2915@pseudogene>

Hi Alan,

That was indeed the problem - pkgconfig was installed, but my
autoconf/automake/libtool installations are in a non-standard location
so as not to interfere with the OS packaged versions. These use a
different share/aclocal directory, which did not contain pgk.m4....

Many thanks,
James
 
On Wed, Dec 08, 2010 at 12:45:55PM +0000, ajb at ebi.ac.uk wrote:
> Hello James,
> 
> There is currently a dependency on pkgconfig in CVS. You are missing
> the pkg.m4 file on your system. In CentOS you can probably get it by
> installing the pkgconfig RPM (which I can see exists for CentOS
> using a google search).
> 
> I'll have a look at this after I return from holiday in the new year.
> 
> HTH
> 
> Alan
> 
> 
> > Hello,
> >
> > I'm trying to build a clean CVS checkout of the emboss code, but the
> > configure script generated by autoconf contains a syntax error:
> >
> > checking for HPDF_New in -lhpdf... yes
> > PDF support found
> > checking whether to look for gsoap support... no
> > checking whether to look for axis2c support... ./configure: line 13496:
> > syntax error near unexpected token `AXIS2C,axis2c,'
> > ./configure: line 13496: `    PKG_CHECK_MODULES(AXIS2C,axis2c,'
> >
> >
> > The relevent section of configure looks like:
> >
> > ======================================================================
> > if test "x$with_axis2c" != xno; then :
> >
> >     { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
> > $as_echo "yes" >&6; }
> >     if test "x$with_axis2c" != "xyes" ; then
> >         ALT_HOME=$with_axis2c
> >         if test ! -d "${ALT_HOME}" ; then
> >           as_fn_error $? "No such axis2c directory (${ALT_HOME})"
> > "$LINENO" 5
> >         fi
> >          export
> > PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$ALT_HOME/lib/pkgconfig"
> >     else
> >         ALT_HOME="/usr"
> >     fi
> >
> >     PKG_CHECK_MODULES(AXIS2C,axis2c,
> >
> >         AXIS2C_CPPFLAGS=${AXIS2C_CFLAGS}
> >         AXIS2C_LDFLAGS=${AXIS2C_LIBS}
> >     ,
> >
> >         echo pkg-config axis2c detection failed
> >     )
> >
> > ======================================================================
> >
> > I'm using the following versions on a CentOS5.5 machine:
> >
> > autoconf (GNU Autoconf) 2.68
> > ltmain.sh (GNU libtool) 2.2
> > automake (GNU automake) 1.9.6
> >
> > and after checking out the code ran:
> >
> > autoreconf -fiv
> > ./configure --enable-warnings --disable-shared --enable-debug
> >
> > Does anyone have any idea if the current CVS version is sick, or if this
> > is a problem with my environment/versions etc.?
> >
> > Best Regards,
> > James
> > --
> > Dr. James Abbott
> > Bioinformatics Software Developer
> > Imperial College, London
> > _______________________________________________
> > emboss-dev mailing list
> > emboss-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss-dev
> >
> 
> 

-- 
Dr. James Abbott
Bioinformatics Software Developer
Imperial College, London