diff -Nru librg-utils-perl-1.0.42/aclocal.m4 librg-utils-perl-1.0.43/aclocal.m4 --- librg-utils-perl-1.0.42/aclocal.m4 2011-09-28 13:06:31.000000000 +0000 +++ librg-utils-perl-1.0.43/aclocal.m4 2011-10-28 20:11:56.000000000 +0000 @@ -13,8 +13,8 @@ m4_ifndef([AC_AUTOCONF_VERSION], [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl -m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.68],, -[m4_warning([this file was generated for autoconf 2.68. +m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],, +[m4_warning([this file was generated for autoconf 2.67. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically `autoreconf'.])]) diff -Nru librg-utils-perl-1.0.42/blastpgp_to_saf.pl librg-utils-perl-1.0.43/blastpgp_to_saf.pl --- librg-utils-perl-1.0.42/blastpgp_to_saf.pl 2011-06-30 13:13:51.000000000 +0000 +++ librg-utils-perl-1.0.43/blastpgp_to_saf.pl 2011-10-28 19:58:41.000000000 +0000 @@ -146,6 +146,7 @@ #............................................................ + my $bug_query = 0; undef @alignedNames; undef @alignedids; $Score_count=0; undef %multi_aligned; $global_count=0; undef %rdb_lines; #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @@ -252,8 +253,8 @@ } } #----------------------------------------------------------------------------------------------------- - # lkajan: below is a probably blast bug, with the Query: 0 line... - # 0 1 2 + # lkajan: below is probably a blast bug, with the Query: 0 line... + # 0 1 2 # Query: 0 ---- # # Sbjct: 64 PAQG 67 @@ -272,13 +273,24 @@ #Sbjct 1 MDPGECTCMSGGICICGDNCKCTTCNCKTCRKSCCPCCPPGCAKCAQGCICKGGSDKCSC 60 # lkajan: do not confuse with 'Query= MT4_HUMAN' - this may appear in blast+ after each round header - if($bline=~/^Query:?\s+\d+/o){ @tmp=split(/\s+/o,$bline); undef @aligned; undef @inserted_query; - $beg=$tmp[1]-1; if( $beg == -1 ) { $end = -1; } else { $end=$tmp[3]-1; } - if (! defined $endings{$Score_count}[0] || $endings{$Score_count}[0] < 0 ){ $endings{$Score_count}[0]=$beg;} - $endings{$Score_count}[1]=$end; - if( defined($tmp[2]) ){ @inserted_query=split(//o,$tmp[2]); } - } - if($bline=~/^Sbjct/o){ + if($bline=~/^Query:?\s+\d+/o) + { + @tmp=split(/\s+/o,$bline); + if( $tmp[1] != 0 ) + { + $bug_query = 0; + undef @aligned; undef @inserted_query; + $beg=$tmp[1]-1; $end=$tmp[3]-1; + if (! defined $endings{$Score_count}[0] || $endings{$Score_count}[0] < 0 ){ $endings{$Score_count}[0]=$beg;} + $endings{$Score_count}[1]=$end; + @inserted_query=split(//o,$tmp[2]); + } + else + { + $bug_query = 1; + } + } + if( !$bug_query && $bline =~ /^Sbjct/o ){ @tmp=split(/\s+/o,$bline); @aligned=split(//o,$tmp[2]); #getting rid of insertions at query sequence @@ -290,7 +302,7 @@ $tmp_seq[$local_counter]=$aligned[$it]; $local_counter++; } - } + } #@aligned=@tmp_seq; #------------------------------------------- #+++++++++++= @@ -486,4 +498,4 @@ -# vim:ai: +# vim:ai:ts=4: diff -Nru librg-utils-perl-1.0.42/ChangeLog librg-utils-perl-1.0.43/ChangeLog --- librg-utils-perl-1.0.42/ChangeLog 2011-09-28 13:06:23.000000000 +0000 +++ librg-utils-perl-1.0.43/ChangeLog 2011-10-28 20:10:55.000000000 +0000 @@ -1,4 +1,11 @@ -librg-utils-perl (1.0.42) UNRELEASED; urgency=low +librg-utils-perl (1.0.43) unstable; urgency=low + + * librg-utils-perl.spec.in added + * fixed warnings caused by buggy blast output + + -- Laszlo Kajan Fri, 28 Oct 2011 22:10:33 +0200 + +librg-utils-perl (1.0.42) unstable; urgency=low * deprecated defined %hash are rewritten * deprecated $[ are silenced with no warnings 'deprecated'; diff -Nru librg-utils-perl-1.0.42/configure librg-utils-perl-1.0.43/configure --- librg-utils-perl-1.0.42/configure 2011-09-28 13:06:33.000000000 +0000 +++ librg-utils-perl-1.0.43/configure 2011-10-28 20:11:57.000000000 +0000 @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.68 for librg-utils-perl 1.0.42. +# Generated by GNU Autoconf 2.67 for librg-utils-perl 1.0.43. # # Report bugs to . # @@ -91,7 +91,6 @@ IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -as_myself= case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -216,18 +215,11 @@ # We cannot yet assume a decent shell, so we have to provide a # neutralization value for shells without unset; and this also # works around shells that cannot unset nonexistent variables. - # Preserve -v and -x to the replacement shell. BASH_ENV=/dev/null ENV=/dev/null (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV export CONFIG_SHELL - case $- in # (((( - *v*x* | *x*v* ) as_opts=-vx ;; - *v* ) as_opts=-v ;; - *x* ) as_opts=-x ;; - * ) as_opts= ;; - esac - exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"} + exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} fi if test x$as_have_required = xno; then : @@ -560,8 +552,8 @@ # Identity of this package. PACKAGE_NAME='librg-utils-perl' PACKAGE_TARNAME='librg-utils-perl' -PACKAGE_VERSION='1.0.42' -PACKAGE_STRING='librg-utils-perl 1.0.42' +PACKAGE_VERSION='1.0.43' +PACKAGE_STRING='librg-utils-perl 1.0.43' PACKAGE_BUGREPORT='https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librg-utils-perl' PACKAGE_URL='' @@ -1040,7 +1032,7 @@ $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2 expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null && $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2 - : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}" + : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option} ;; esac @@ -1178,7 +1170,7 @@ # 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 librg-utils-perl 1.0.42 to adapt to many kinds of systems. +\`configure' configures librg-utils-perl 1.0.43 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1245,7 +1237,7 @@ if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of librg-utils-perl 1.0.42:";; + short | recursive ) echo "Configuration of librg-utils-perl 1.0.43:";; esac cat <<\_ACEOF @@ -1312,8 +1304,8 @@ test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -librg-utils-perl configure 1.0.42 -generated by GNU Autoconf 2.68 +librg-utils-perl configure 1.0.43 +generated by GNU Autoconf 2.67 Copyright (C) 2010 Free Software Foundation, Inc. This configure script is free software; the Free Software Foundation @@ -1329,8 +1321,8 @@ This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by librg-utils-perl $as_me 1.0.42, which was -generated by GNU Autoconf 2.68. Invocation command line was +It was created by librg-utils-perl $as_me 1.0.43, which was +generated by GNU Autoconf 2.67. Invocation command line was $ $0 $@ @@ -1588,7 +1580,7 @@ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "failed to load site script $ac_site_file -See \`config.log' for more details" "$LINENO" 5; } +See \`config.log' for more details" "$LINENO" 5 ; } fi done @@ -1727,7 +1719,7 @@ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5 $as_echo_n "checking for a BSD-compatible install... " >&6; } if test -z "$INSTALL"; then -if ${ac_cv_path_install+:} false; then : +if test "${ac_cv_path_install+set}" = set; then : $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -1814,11 +1806,11 @@ ' case `pwd` in *[\\\"\#\$\&\'\`$am_lf]*) - as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5;; + as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;; esac case $srcdir in *[\\\"\#\$\&\'\`$am_lf\ \ ]*) - as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;; + as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;; esac # Do `set' in a subshell so we don't clobber the current shell's @@ -1904,7 +1896,7 @@ set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if ${ac_cv_prog_STRIP+:} false; then : +if test "${ac_cv_prog_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then @@ -1944,7 +1936,7 @@ set dummy strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if ${ac_cv_prog_ac_ct_STRIP+:} false; then : +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then @@ -1997,7 +1989,7 @@ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5 $as_echo_n "checking for a thread-safe mkdir -p... " >&6; } if test -z "$MKDIR_P"; then - if ${ac_cv_path_mkdir+:} false; then : + if test "${ac_cv_path_mkdir+set}" = set; then : $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2048,7 +2040,7 @@ set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if ${ac_cv_prog_AWK+:} false; then : +if test "${ac_cv_prog_AWK+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$AWK"; then @@ -2088,7 +2080,7 @@ $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; } set x ${MAKE-make} ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'` -if eval \${ac_cv_prog_make_${ac_make}_set+:} false; then : +if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then : $as_echo_n "(cached) " >&6 else cat >conftest.make <<\_ACEOF @@ -2146,7 +2138,7 @@ # Define the identity of the package. PACKAGE='librg-utils-perl' - VERSION='1.0.42' + VERSION='1.0.43' cat >>confdefs.h <<_ACEOF @@ -2186,7 +2178,7 @@ -ac_config_files="$ac_config_files Makefile Build.PL lib/Makefile lib/RG/Makefile lib/RG/Utils/Makefile mat/Makefile" +ac_config_files="$ac_config_files Makefile Build.PL librg-utils-perl.spec lib/Makefile lib/RG/Makefile lib/RG/Utils/Makefile mat/Makefile" @@ -2258,21 +2250,10 @@ :end' >>confcache if diff "$cache_file" confcache >/dev/null 2>&1; then :; else if test -w "$cache_file"; then - if test "x$cache_file" != "x/dev/null"; then + test "x$cache_file" != "x/dev/null" && { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 $as_echo "$as_me: updating cache $cache_file" >&6;} - if test ! -f "$cache_file" || test -h "$cache_file"; then - cat confcache >"$cache_file" - else - case $cache_file in #( - */* | ?:*) - mv -f confcache "$cache_file"$$ && - mv -f "$cache_file"$$ "$cache_file" ;; #( - *) - mv -f confcache "$cache_file" ;; - esac - fi - fi + cat confcache >$cache_file else { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} @@ -2341,7 +2322,7 @@ -: "${CONFIG_STATUS=./config.status}" +: ${CONFIG_STATUS=./config.status} ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" @@ -2442,7 +2423,6 @@ IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -as_myself= case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2749,8 +2729,8 @@ # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by librg-utils-perl $as_me 1.0.42, which was -generated by GNU Autoconf 2.68. Invocation command line was +This file was extended by librg-utils-perl $as_me 1.0.43, which was +generated by GNU Autoconf 2.67. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -2802,8 +2782,8 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -librg-utils-perl config.status 1.0.42 -configured by $0, generated by GNU Autoconf 2.68, +librg-utils-perl config.status 1.0.43 +configured by $0, generated by GNU Autoconf 2.67, with options \\"\$ac_cs_config\\" Copyright (C) 2010 Free Software Foundation, Inc. @@ -2917,12 +2897,13 @@ case $ac_config_target in "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; "Build.PL") CONFIG_FILES="$CONFIG_FILES Build.PL" ;; + "librg-utils-perl.spec") CONFIG_FILES="$CONFIG_FILES librg-utils-perl.spec" ;; "lib/Makefile") CONFIG_FILES="$CONFIG_FILES lib/Makefile" ;; "lib/RG/Makefile") CONFIG_FILES="$CONFIG_FILES lib/RG/Makefile" ;; "lib/RG/Utils/Makefile") CONFIG_FILES="$CONFIG_FILES lib/RG/Utils/Makefile" ;; "mat/Makefile") CONFIG_FILES="$CONFIG_FILES mat/Makefile" ;; - *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;; + *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;; esac done @@ -2943,10 +2924,9 @@ # after its creation but before its name has been assigned to `$tmp'. $debug || { - tmp= ac_tmp= + tmp= trap 'exit_status=$? - : "${ac_tmp:=$tmp}" - { test ! -d "$ac_tmp" || rm -fr "$ac_tmp"; } && exit $exit_status + { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status ' 0 trap 'as_fn_exit 1' 1 2 13 15 } @@ -2954,13 +2934,12 @@ { tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && - test -d "$tmp" + test -n "$tmp" && test -d "$tmp" } || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") } || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 -ac_tmp=$tmp # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. @@ -2982,7 +2961,7 @@ ac_cs_awk_cr=$ac_cr fi -echo 'BEGIN {' >"$ac_tmp/subs1.awk" && +echo 'BEGIN {' >"$tmp/subs1.awk" && _ACEOF @@ -3010,7 +2989,7 @@ rm -f conf$$subs.sh cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 -cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK && +cat >>"\$tmp/subs1.awk" <<\\_ACAWK && _ACEOF sed -n ' h @@ -3058,7 +3037,7 @@ rm -f conf$$subs.awk cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACAWK -cat >>"\$ac_tmp/subs1.awk" <<_ACAWK && +cat >>"\$tmp/subs1.awk" <<_ACAWK && for (key in S) S_is_set[key] = 1 FS = "" @@ -3090,7 +3069,7 @@ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g" else cat -fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \ +fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 _ACEOF @@ -3130,7 +3109,7 @@ esac case $ac_mode$ac_tag in :[FHL]*:*);; - :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;; + :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -3149,7 +3128,7 @@ for ac_f do case $ac_f in - -) ac_f="$ac_tmp/stdin";; + -) ac_f="$tmp/stdin";; *) # Look for the file first in the build tree, then in the source tree # (if the path is not absolute). The absolute path cannot be DOS-style, # because $ac_f cannot contain `:'. @@ -3158,7 +3137,7 @@ [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;; + as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac as_fn_append ac_file_inputs " '$ac_f'" @@ -3184,8 +3163,8 @@ esac case $ac_tag in - *:-:* | *:-) cat >"$ac_tmp/stdin" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; + *:-:* | *:-) cat >"$tmp/stdin" \ + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; esac ;; esac @@ -3321,22 +3300,21 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t $ac_datarootdir_hack " -eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \ - >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5 +eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \ + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && - { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } && - { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \ - "$ac_tmp/out"`; test -z "$ac_out"; } && + { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } && + { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } && { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&2;} - rm -f "$ac_tmp/stdin" + rm -f "$tmp/stdin" case $ac_file in - -) cat "$ac_tmp/out" && rm -f "$ac_tmp/out";; - *) rm -f "$ac_file" && mv "$ac_tmp/out" "$ac_file";; + -) cat "$tmp/out" && rm -f "$tmp/out";; + *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; esac \ || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; diff -Nru librg-utils-perl-1.0.42/configure.ac librg-utils-perl-1.0.43/configure.ac --- librg-utils-perl-1.0.42/configure.ac 2011-09-28 13:05:24.000000000 +0000 +++ librg-utils-perl-1.0.43/configure.ac 2011-10-28 20:09:49.000000000 +0000 @@ -1,8 +1,8 @@ -AC_INIT([librg-utils-perl], [1.0.42], [https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librg-utils-perl]) +AC_INIT([librg-utils-perl], [1.0.43], [https://rostlab.org/cgi-bin/bugzilla3/enter_bug.cgi?product=librg-utils-perl]) # remember to update version number in Build.PL # PERLLIBDIR=$(eval "`perl -V:installvendorlib`"; echo $installvendorlib) AM_INIT_AUTOMAKE -AC_CONFIG_FILES([Makefile] [Build.PL] [lib/Makefile] [lib/RG/Makefile] [lib/RG/Utils/Makefile] [mat/Makefile]) +AC_CONFIG_FILES([Makefile] [Build.PL] [librg-utils-perl.spec] [lib/Makefile] [lib/RG/Makefile] [lib/RG/Utils/Makefile] [mat/Makefile]) AC_SUBST(INSTALL_BASE_ARG) if test "x$prefix" != "x/usr"; then diff -Nru librg-utils-perl-1.0.42/debian/changelog librg-utils-perl-1.0.43/debian/changelog --- librg-utils-perl-1.0.42/debian/changelog 2011-09-28 16:32:33.000000000 +0000 +++ librg-utils-perl-1.0.43/debian/changelog 2011-11-28 15:03:57.000000000 +0000 @@ -1,3 +1,9 @@ +librg-utils-perl (1.0.43-1) unstable; urgency=low + + * New upstream release + + -- Laszlo Kajan Fri, 28 Oct 2011 22:20:27 +0200 + librg-utils-perl (1.0.42-1) unstable; urgency=low * Initial release (Closes: #643630) diff -Nru librg-utils-perl-1.0.42/librg-utils-perl.spec librg-utils-perl-1.0.43/librg-utils-perl.spec --- librg-utils-perl-1.0.42/librg-utils-perl.spec 2011-07-10 14:02:45.000000000 +0000 +++ librg-utils-perl-1.0.43/librg-utils-perl.spec 1970-01-01 00:00:00.000000000 +0000 @@ -1,58 +0,0 @@ -Summary: a set of wrappers and conversion utilities for bioinformatics databases -Name: librg-utils-perl -Version: 1.0.41 -Release: 1 -License: GPL -Group: Applications/Science -Source: ftp://rostlab.org/%{name}/%{name}-%{version}.tar.gz -URL: http://rostlab.org/ -BuildArch: noarch -BuildRoot: %{_tmppath}/%{name}-%{version}-root -BuildRequires: perl -Requires: perl-List-MoreUtils, profphd-utils - -%description - This package contains assorted tools like: - . - * blast2saf.pl, blastpgp_to_saf.pl, conv_hssp2saf.pl, copf.pl, hssp_filter.pl, - safFilterRed.pl - . - and modules like: - . - * RG:Utils::Conv_hssp2saf RG:Utils::Copf RG:Utils::Hssp_filter - -%prep -%setup -q - -%build -%configure PERLLIBDIR=%{perl_vendorlib} -make - -%install -rm -rf $RPM_BUILD_ROOT -make DESTDIR=${RPM_BUILD_ROOT} install - -%clean -rm -rf $RPM_BUILD_ROOT - -%files -%defattr(-,root,root) -%doc AUTHORS -%doc COPYING -%{_mandir}/*/* -%{_datadir}/%{name}/* -%{perl_vendorlib}/RG/Utils/* - -%changelog -* Mon Jun 27 2011 Laszlo Kajan - 1.0.41-1 -- new upstream -* Mon Jun 27 2011 Laszlo Kajan - 1.0.39-1 -- new upstream -* Wed Jun 22 2011 Laszlo Kajan - 1.0.38-1 -- new upstream -* Tue Jun 21 2011 Laszlo Kajan - 1.0.37-1 -- new upstream -* Tue Jun 21 2011 Laszlo Kajan - 1.0.36-2 -- spec file in dist root, DESTDIR on install -* Wed Jun 16 2011 Guy Yachdav - 1.0.36-1 -- Initial build. diff -Nru librg-utils-perl-1.0.42/librg-utils-perl.spec.in librg-utils-perl-1.0.43/librg-utils-perl.spec.in --- librg-utils-perl-1.0.42/librg-utils-perl.spec.in 1970-01-01 00:00:00.000000000 +0000 +++ librg-utils-perl-1.0.43/librg-utils-perl.spec.in 2011-10-28 20:07:17.000000000 +0000 @@ -0,0 +1,60 @@ +Summary: a set of wrappers and conversion utilities for bioinformatics databases +Name: librg-utils-perl +Version: @VERSION@ +Release: 1 +License: GPL +Group: Applications/Science +Source: ftp://rostlab.org/%{name}/%{name}-%{version}.tar.gz +URL: http://rostlab.org/ +BuildArch: noarch +BuildRoot: %{_tmppath}/%{name}-%{version}-root +BuildRequires: perl +Requires: perl-List-MoreUtils, profphd-utils + +%description + This package contains assorted tools like: + . + * blast2saf.pl, blastpgp_to_saf.pl, conv_hssp2saf.pl, copf.pl, hssp_filter.pl, + safFilterRed.pl + . + and modules like: + . + * RG:Utils::Conv_hssp2saf RG:Utils::Copf RG:Utils::Hssp_filter + +%prep +%setup -q + +%build +%configure PERLLIBDIR=%{perl_vendorlib} +make + +%install +rm -rf $RPM_BUILD_ROOT +make DESTDIR=${RPM_BUILD_ROOT} install + +%clean +rm -rf $RPM_BUILD_ROOT + +%files +%defattr(-,root,root) +%doc AUTHORS +%doc COPYING +%{_mandir}/*/* +%{_datadir}/%{name}/* +%{perl_vendorlib}/RG/Utils/* + +%changelog +* Fri Oct 28 2011 Laszlo Kajan - 1.0.42-1 +- new upstream +* Mon Jun 27 2011 Laszlo Kajan - 1.0.41-1 +- new upstream +* Mon Jun 27 2011 Laszlo Kajan - 1.0.39-1 +- new upstream +* Wed Jun 22 2011 Laszlo Kajan - 1.0.38-1 +- new upstream +* Tue Jun 21 2011 Laszlo Kajan - 1.0.37-1 +- new upstream +* Tue Jun 21 2011 Laszlo Kajan - 1.0.36-2 +- spec file in dist root, DESTDIR on install +* Wed Jun 16 2011 Guy Yachdav - 1.0.36-1 +- Initial build. diff -Nru librg-utils-perl-1.0.42/Makefile.am librg-utils-perl-1.0.43/Makefile.am --- librg-utils-perl-1.0.42/Makefile.am 2011-09-28 13:09:06.000000000 +0000 +++ librg-utils-perl-1.0.43/Makefile.am 2011-10-28 20:18:48.000000000 +0000 @@ -1,6 +1,6 @@ SUBDIRS = lib mat -dist_noinst_DATA = Build.PL.in $(PACKAGE).spec +dist_noinst_DATA = Build.PL.in $(PACKAGE).spec.in dist_noinst_SCRIPTS = dist_pkgdata_SCRIPTS = blast2saf.pl blastpgp_to_saf.pl conv_hssp2saf.pl copf.pl dbSwiss hssp_filter.pl safFilterRed.pl @@ -16,10 +16,10 @@ if [ -e Build ]; then perl Build clean && rm -f Build build-stamp; fi distclean-local: - rm -rf _build MYMETA.yml + rm -rf _build MYMETA.yml MANIFEST MANIFEST.SKIP.bak MANIFEST.SKIP build-stamp: Build.PL - perl $(srcdir)/Build.PL installdirs=vendor && perl Build manifest && perl Build && touch build-stamp + perl Build.PL installdirs=vendor && perl Build manifest && perl Build && touch build-stamp install-data-local: perl Build install destdir=$(DESTDIR) $(INSTALL_BASE_ARG) create_packlist=0 diff -Nru librg-utils-perl-1.0.42/Makefile.in librg-utils-perl-1.0.43/Makefile.in --- librg-utils-perl-1.0.42/Makefile.in 2011-09-28 13:09:12.000000000 +0000 +++ librg-utils-perl-1.0.43/Makefile.in 2011-10-28 20:18:50.000000000 +0000 @@ -37,8 +37,9 @@ DIST_COMMON = README $(am__configure_deps) $(dist_noinst_DATA) \ $(dist_noinst_SCRIPTS) $(dist_pkgdata_SCRIPTS) \ $(srcdir)/Build.PL.in $(srcdir)/Makefile.am \ - $(srcdir)/Makefile.in $(top_srcdir)/configure AUTHORS COPYING \ - ChangeLog INSTALL NEWS install-sh missing + $(srcdir)/Makefile.in $(srcdir)/librg-utils-perl.spec.in \ + $(top_srcdir)/configure AUTHORS COPYING ChangeLog INSTALL NEWS \ + install-sh missing ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/configure.ac am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ @@ -46,7 +47,7 @@ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ configure.lineno config.status.lineno mkinstalldirs = $(install_sh) -d -CONFIG_CLEAN_FILES = Build.PL +CONFIG_CLEAN_FILES = Build.PL librg-utils-perl.spec CONFIG_CLEAN_VPATH_FILES = am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; am__vpath_adj = case $$p in \ @@ -204,7 +205,7 @@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ SUBDIRS = lib mat -dist_noinst_DATA = Build.PL.in $(PACKAGE).spec +dist_noinst_DATA = Build.PL.in $(PACKAGE).spec.in dist_noinst_SCRIPTS = dist_pkgdata_SCRIPTS = blast2saf.pl blastpgp_to_saf.pl conv_hssp2saf.pl copf.pl dbSwiss hssp_filter.pl safFilterRed.pl man_MANS = dbSwiss.1 @@ -249,6 +250,8 @@ $(am__aclocal_m4_deps): Build.PL: $(top_builddir)/config.status $(srcdir)/Build.PL.in cd $(top_builddir) && $(SHELL) ./config.status $@ +librg-utils-perl.spec: $(top_builddir)/config.status $(srcdir)/librg-utils-perl.spec.in + cd $(top_builddir) && $(SHELL) ./config.status $@ install-dist_pkgdataSCRIPTS: $(dist_pkgdata_SCRIPTS) @$(NORMAL_INSTALL) test -z "$(pkgdatadir)" || $(MKDIR_P) "$(DESTDIR)$(pkgdatadir)" @@ -820,10 +823,10 @@ if [ -e Build ]; then perl Build clean && rm -f Build build-stamp; fi distclean-local: - rm -rf _build MYMETA.yml + rm -rf _build MYMETA.yml MANIFEST MANIFEST.SKIP.bak MANIFEST.SKIP build-stamp: Build.PL - perl $(srcdir)/Build.PL installdirs=vendor && perl Build manifest && perl Build && touch build-stamp + perl Build.PL installdirs=vendor && perl Build manifest && perl Build && touch build-stamp install-data-local: perl Build install destdir=$(DESTDIR) $(INSTALL_BASE_ARG) create_packlist=0