Commit f8e5b25c authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.99d+dfsg

parent 8a2d935a

ChangeLog

+24 −0
Original line number Diff line number Diff line 
2017-02-21  Nicolas Joly  <njoly@pasteur.fr>



	* configure.ac: Bump version to 0.99d.



2017-02-21  Nicolas Joly  <njoly@pasteur.fr>



	* test/embl.sh: Exercize long sequence name.



2017-02-21  Nicolas Joly  <njoly@pasteur.fr>



	* test/genbank.sh: Exercize long sequence name.



2017-02-21  Nicolas Joly  <njoly@pasteur.fr>



	* lib/sequence/sprotl.l: Allow long sequence names (up to 75

	characters).

	* test/sprot.sh: Exercize it.



2017-02-21  Nicolas Joly  <njoly@pasteur.fr>



	* lib/sequence/embl*.[ly]: Reject sequence names that are followed

	by a space character.

	* test/embl.sh: Exercize it.



2015-12-02  Nicolas Joly  <njoly@pasteur.fr>



	* lib/sequence/sprotl.l: Adjust TrEmbl allowed entry names.

Makefile.in

+1 −1
Original line number Diff line number Diff line
@@ -161,7 +161,7 @@ CSCOPE = cscope 
DIST_SUBDIRS = $(SUBDIRS)

am__DIST_COMMON = $(srcdir)/Makefile.in AUTHORS COPYING ChangeLog \

	INSTALL NEWS README TODO compile config.guess config.sub \

	install-sh ltmain.sh missing mkinstalldirs ylwrap

	depcomp install-sh ltmain.sh missing mkinstalldirs ylwrap

DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)

distdir = $(PACKAGE)-$(VERSION)

top_distdir = $(distdir)

configure

+210 −13
Original line number Diff line number Diff line 
#! /bin/sh

# Guess values for system-dependent variables and create Makefiles.

# Generated by GNU Autoconf 2.69 for squizz 0.99c.

# Generated by GNU Autoconf 2.69 for squizz 0.99d.

#

#

# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -587,8 +587,8 @@ MAKEFLAGS= 
# Identity of this package.

PACKAGE_NAME='squizz'

PACKAGE_TARNAME='squizz'

PACKAGE_VERSION='0.99c'

PACKAGE_STRING='squizz 0.99c'

PACKAGE_VERSION='0.99d'

PACKAGE_STRING='squizz 0.99d'

PACKAGE_BUGREPORT=''

PACKAGE_URL=''
@@ -765,6 +765,7 @@ with_aix_soname 
with_gnu_ld

with_sysroot

enable_libtool_lock

enable_largefile

'

      ac_precious_vars='build_alias

host_alias
@@ -1318,7 +1319,7 @@ if test "$ac_init_help" = "long"; then 
  # Omit some internal or obsolete options to make the list less imposing.

  # This message is too long to be a string in the A/UX 3.1 sh.

  cat <<_ACEOF

\`configure' configures squizz 0.99c to adapt to many kinds of systems.

\`configure' configures squizz 0.99d to adapt to many kinds of systems.



Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1388,7 +1389,7 @@ fi 


if test -n "$ac_init_help"; then

  case $ac_init_help in

     short | recursive ) echo "Configuration of squizz 0.99c:";;

     short | recursive ) echo "Configuration of squizz 0.99d:";;

   esac

  cat <<\_ACEOF
@@ -1407,6 +1408,7 @@ Optional Features: 
  --enable-fast-install[=PKGS]

                          optimize for fast installation [default=yes]

  --disable-libtool-lock  avoid locking (might break parallel builds)

  --disable-largefile     omit support for large files



Optional Packages:

  --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
@@ -1504,7 +1506,7 @@ fi 
test -n "$ac_init_help" && exit $ac_status

if $ac_init_version; then

  cat <<\_ACEOF

squizz configure 0.99c

squizz configure 0.99d

generated by GNU Autoconf 2.69



Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2160,7 +2162,7 @@ cat >config.log <<_ACEOF 
This file contains any messages produced by compilers while

running configure, to aid debugging if configure makes a mistake.



It was created by squizz $as_me 0.99c, which was

It was created by squizz $as_me 0.99d, which was

generated by GNU Autoconf 2.69.  Invocation command line was



  $ $0 $@
@@ -3023,7 +3025,7 @@ fi 


# Define the identity of the package.

 PACKAGE='squizz'

 VERSION='0.99c'

 VERSION='0.99d'





cat >>confdefs.h <<_ACEOF
@@ -12801,8 +12803,6 @@ $as_echo "#define HAVE_FSEEKO 1" >>confdefs.h 


fi



#AC_FUNC_MALLOC

#AC_FUNC_REALLOC

for ac_func in strftime

do :

  ac_fn_c_check_func "$LINENO" "strftime" "ac_cv_func_strftime"
@@ -12872,8 +12872,205 @@ done 




# Add 64-bits file support on some hosts

# Check whether --enable-largefile was given.

if test "${enable_largefile+set}" = set; then :

  enableval=$enable_largefile;

fi



if test "$enable_largefile" != no; then



  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for special C compiler options needed for large files" >&5

$as_echo_n "checking for special C compiler options needed for large files... " >&6; }

if ${ac_cv_sys_largefile_CC+:} false; then :

  $as_echo_n "(cached) " >&6

else

  ac_cv_sys_largefile_CC=no

     if test "$GCC" != yes; then

       ac_save_CC=$CC

       while :; do

	 # IRIX 6.2 and later do not support large files by default,

	 # so use the C compiler's -n32 option if that helps.

	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext

/* end confdefs.h.  */

#include <sys/types.h>

 /* Check that off_t can represent 2**63 - 1 correctly.

    We can't simply define LARGE_OFF_T to be 9223372036854775807,

    since some C++ compilers masquerading as C compilers

    incorrectly reject 9223372036854775807.  */

#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))

  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721

		       && LARGE_OFF_T % 2147483647 == 1)

		      ? 1 : -1];

int

main ()

{



  ;

  return 0;

}

_ACEOF

	 if ac_fn_c_try_compile "$LINENO"; then :

  break

fi

rm -f core conftest.err conftest.$ac_objext

	 CC="$CC -n32"

	 if ac_fn_c_try_compile "$LINENO"; then :

  ac_cv_sys_largefile_CC=' -n32'; break

fi

rm -f core conftest.err conftest.$ac_objext

	 break

       done

       CC=$ac_save_CC

       rm -f conftest.$ac_ext

    fi

fi

{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_largefile_CC" >&5

$as_echo "$ac_cv_sys_largefile_CC" >&6; }

  if test "$ac_cv_sys_largefile_CC" != no; then

    CC=$CC$ac_cv_sys_largefile_CC

  fi



  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for _FILE_OFFSET_BITS value needed for large files" >&5

$as_echo_n "checking for _FILE_OFFSET_BITS value needed for large files... " >&6; }

if ${ac_cv_sys_file_offset_bits+:} false; then :

  $as_echo_n "(cached) " >&6

else

  while :; do

  cat confdefs.h - <<_ACEOF >conftest.$ac_ext

/* end confdefs.h.  */

#include <sys/types.h>

 /* Check that off_t can represent 2**63 - 1 correctly.

    We can't simply define LARGE_OFF_T to be 9223372036854775807,

    since some C++ compilers masquerading as C compilers

    incorrectly reject 9223372036854775807.  */

#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))

  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721

		       && LARGE_OFF_T % 2147483647 == 1)

		      ? 1 : -1];

int

main ()

{



  ;

  return 0;

}

_ACEOF

if ac_fn_c_try_compile "$LINENO"; then :

  ac_cv_sys_file_offset_bits=no; break

fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext

  cat confdefs.h - <<_ACEOF >conftest.$ac_ext

/* end confdefs.h.  */

#define _FILE_OFFSET_BITS 64

#include <sys/types.h>

 /* Check that off_t can represent 2**63 - 1 correctly.

    We can't simply define LARGE_OFF_T to be 9223372036854775807,

    since some C++ compilers masquerading as C compilers

    incorrectly reject 9223372036854775807.  */

#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))

  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721

		       && LARGE_OFF_T % 2147483647 == 1)

		      ? 1 : -1];

int

main ()

{



  ;

  return 0;

}

_ACEOF

if ac_fn_c_try_compile "$LINENO"; then :

  ac_cv_sys_file_offset_bits=64; break

fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext

  ac_cv_sys_file_offset_bits=unknown

  break

done

fi

{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_file_offset_bits" >&5

$as_echo "$ac_cv_sys_file_offset_bits" >&6; }

case $ac_cv_sys_file_offset_bits in #(

  no | unknown) ;;

  *)

cat >>confdefs.h <<_ACEOF

#define _FILE_OFFSET_BITS $ac_cv_sys_file_offset_bits

_ACEOF

;;

esac

rm -rf conftest*

  if test $ac_cv_sys_file_offset_bits = unknown; then

    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for _LARGE_FILES value needed for large files" >&5

$as_echo_n "checking for _LARGE_FILES value needed for large files... " >&6; }

if ${ac_cv_sys_large_files+:} false; then :

  $as_echo_n "(cached) " >&6

else

  while :; do

  cat confdefs.h - <<_ACEOF >conftest.$ac_ext

/* end confdefs.h.  */

#include <sys/types.h>

 /* Check that off_t can represent 2**63 - 1 correctly.

    We can't simply define LARGE_OFF_T to be 9223372036854775807,

    since some C++ compilers masquerading as C compilers

    incorrectly reject 9223372036854775807.  */

#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))

  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721

		       && LARGE_OFF_T % 2147483647 == 1)

		      ? 1 : -1];

int

main ()

{



$as_echo "#define _FILE_OFFSET_BITS 64" >>confdefs.h

  ;

  return 0;

}

_ACEOF

if ac_fn_c_try_compile "$LINENO"; then :

  ac_cv_sys_large_files=no; break

fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext

  cat confdefs.h - <<_ACEOF >conftest.$ac_ext

/* end confdefs.h.  */

#define _LARGE_FILES 1

#include <sys/types.h>

 /* Check that off_t can represent 2**63 - 1 correctly.

    We can't simply define LARGE_OFF_T to be 9223372036854775807,

    since some C++ compilers masquerading as C compilers

    incorrectly reject 9223372036854775807.  */

#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))

  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721

		       && LARGE_OFF_T % 2147483647 == 1)

		      ? 1 : -1];

int

main ()

{



  ;

  return 0;

}

_ACEOF

if ac_fn_c_try_compile "$LINENO"; then :

  ac_cv_sys_large_files=1; break

fi

rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext

  ac_cv_sys_large_files=unknown

  break

done

fi

{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_large_files" >&5

$as_echo "$ac_cv_sys_large_files" >&6; }

case $ac_cv_sys_large_files in #(

  no | unknown) ;;

  *)

cat >>confdefs.h <<_ACEOF

#define _LARGE_FILES $ac_cv_sys_large_files

_ACEOF

;;

esac

rm -rf conftest*

  fi





fi





# Compatibility
@@ -13413,7 +13610,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 
# report actual input values of CONFIG_FILES etc. instead of their

# values after options handling.

ac_log="

This file was extended by squizz $as_me 0.99c, which was

This file was extended by squizz $as_me 0.99d, which was

generated by GNU Autoconf 2.69.  Invocation command line was



  CONFIG_FILES    = $CONFIG_FILES
@@ -13479,7 +13676,7 @@ _ACEOF 
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1

ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"

ac_cs_version="\\

squizz config.status 0.99c

squizz config.status 0.99d

configured by $0, generated by GNU Autoconf 2.69,

  with options \\"\$ac_cs_config\\"

configure.ac

+2 −5
Original line number Diff line number Diff line 
# Process this file with autoconf to produce a configure script.

AC_INIT([squizz],[0.99c])

AC_INIT([squizz],[0.99d])

AM_INIT_AUTOMAKE

AC_CONFIG_HEADERS([lib/config.h])

AC_CONFIG_MACRO_DIR([m4])
@@ -33,14 +33,11 @@ AC_TYPE_UINT64_T 


# Checks for library functions.

AC_FUNC_FSEEKO

#AC_FUNC_MALLOC

#AC_FUNC_REALLOC

AC_FUNC_STRFTIME

AC_CHECK_FUNCS([localtime_r strcasecmp strchr strdup strerror])



# Add 64-bits file support on some hosts

AC_DEFINE([_FILE_OFFSET_BITS], [64],

          [Define to 64 for large file support on some hosts])

AC_SYS_LARGEFILE



# Compatibility

test $ac_cv_header_err_h != yes && \

lib/align.h

+3 −3
Original line number Diff line number Diff line 
/* align.h - Generic alignment functions */



#ifndef __ALIGN_H_

#define __ALIGN_H_

#ifndef SQUIZZ_ALIGN_H_

#define SQUIZZ_ALIGN_H_



#include <stdio.h>
@@ -35,5 +35,5 @@ void align_print(FILE *, align_t *, alifmt_t); 


alifmt_t align_format(FILE *);



#endif /* __ALIGN_H_ */

#endif /* SQUIZZ_ALIGN_H_ */