Author: latticetower-guest Date: 2016-08-24 13:37:16 +0000 (Wed, 24 Aug 2016) New Revision: 22713
Added: trunk/packages/rostlab/profphd/trunk/debian/patches/ trunk/packages/rostlab/profphd/trunk/debian/patches/1_remove_defined_array.patch trunk/packages/rostlab/profphd/trunk/debian/patches/2_remove_perlbrew_usage.patch trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch trunk/packages/rostlab/profphd/trunk/debian/patches/4_fix_negative_repeat_count.patch trunk/packages/rostlab/profphd/trunk/debian/patches/series Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog Log: add patches 1-4 to use latest perl 5.22 (for now this is unfinished) Modified: trunk/packages/rostlab/profphd/trunk/debian/changelog =================================================================== --- trunk/packages/rostlab/profphd/trunk/debian/changelog 2016-08-24 13:18:53 UTC (rev 22712) +++ trunk/packages/rostlab/profphd/trunk/debian/changelog 2016-08-24 13:37:16 UTC (rev 22713) @@ -4,6 +4,7 @@ * cme fix dpkg-control * cme fix dpkg-copyright * add hardening in d/rules + * add patches 1-4 to use latest perl 5.22 (UNFINISHED! checking if this works) -- Tatiana Malygina <[email protected]> Fri, 08 Jul 2016 22:46:36 +0300 Added: trunk/packages/rostlab/profphd/trunk/debian/patches/1_remove_defined_array.patch =================================================================== --- trunk/packages/rostlab/profphd/trunk/debian/patches/1_remove_defined_array.patch (rev 0) +++ trunk/packages/rostlab/profphd/trunk/debian/patches/1_remove_defined_array.patch 2016-08-24 13:37:16 UTC (rev 22713) @@ -0,0 +1,703 @@ +Author: Tatiana Malygina <[email protected]> +Description: change defined(@array) to @array to use with perl 5.22 +Last-Update: 2016-08-22 + +--- a/src/prof/embl/scr/lib-col.pl ++++ b/src/prof/embl/scr/lib-col.pl +@@ -338,7 +338,7 @@ + $#dir2=$Lok=0; + return(0,"no input file") if (! defined $fileInLoc); + $chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g; +- $#dir=0 if (! defined @dir); ++ $#dir=0 if (! @dir); + $Lscreen=0 if (! defined $Lscreen); + if (-d $Lscreen) { + @dir=($Lscreen,@dir); +@@ -1070,7 +1070,7 @@ + $#dir2=$Lok=0; + return(0,"no input file") if (! defined $fileInLoc); + $chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g; +- $#dir=0 if (! defined @dir); ++ $#dir=0 if (! @dir); + $Lscreen=0 if (! defined $Lscreen); + if (-d $Lscreen) { + @dir=($Lscreen,@dir); +@@ -1208,7 +1208,7 @@ + # of all numbers wanted (i.e. = $want[M]) + undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around! + +- $#want=0 if (! defined @want); ++ $#want=0 if (! @want); + $LreadAll=0; + # ------------------------------ + # digest input +@@ -1261,7 +1261,7 @@ + # sort the array + @wantNum= sort bynumber (@wantNum); + # too many wanted +- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ ++ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ + $#tmp=0; + foreach $want (@wantNum){ + if ($want <= $locNum[$#locNum]){ +@@ -1695,7 +1695,7 @@ + $ifirLoc=0 if (! defined $ifirLoc || ($ifirLoc eq "*") ); + $ilasLoc=0 if (! defined $ilasLoc || ($ilasLoc eq "*") ); + $chainLoc=0 if (! defined $chainLoc || ($chainLoc eq "*") ); +- $#kwdRd=0 if (! defined @kwdRd); ++ $#kwdRd=0 if (! @kwdRd); + undef %tmp; + if ($#kwdRd>0){ + foreach $tmp(@kwdRd){ +@@ -3518,7 +3518,7 @@ + #------------------------------------------------------------------------------- + $sbrName="lib-br:"."phdHtmGetBest";$fhinLoc="FHIN_"."phdHtmGetBest"; + # check arguments +- return(&errSbr("no input!")) if (! defined @tmp || $#tmp==0); ++ return(&errSbr("no input!")) if (! @tmp || $#tmp==0); + $minLenLoc=18 if ($minLenLoc == 0); + + $max=0; +@@ -5569,7 +5569,7 @@ + # out: $file (id or 0 for error) + #-------------------------------------------------------------------------------- + return($idLoc) if (-e $idLoc); # already existing directory +- $#dirLoc=0 if (! defined @dirLoc); ++ $#dirLoc=0 if (! @dirLoc); + if (! defined $Lscreen){$Lscreen=0;} + elsif (-d $Lscreen) {@dirLoc=($Lscreen,@dirLoc);$Lscreen=0;} + @dirSwissLoc=("/data/swissprot/current/"); # swiss dir's +--- a/src/prof/embl/scr/conv_phd2hssp.pl ++++ b/src/prof/embl/scr/conv_phd2hssp.pl +@@ -310,7 +310,7 @@ + $par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"};}}}} + # ------------------------------ + # push array of output files +- if (! defined @fileOut){$#fileOut=0;} ++ if (! @fileOut){$#fileOut=0;} + foreach $kwd (@kwdDef){ + if ($kwd=~/^fileOut/){ + push(@fileOut,$par{"$kwd"});}} +@@ -327,7 +327,7 @@ + $par{"$kwd"}=$par{"dirWork"}.$par{"$kwd"};}}}} + # ------------------------------ + # array of Work files +- if (! defined @fileWork){$#fileWork=0;} ++ if (! @fileWork){$#fileWork=0;} + foreach $kwd (@kwdDef){ + if (($kwd=~/^file/)&&($kwd!~/^fileIn/)&&($kwd!~/^fileOut/)){ + push(@fileWork,$par{"$kwd"});}} +@@ -511,4 +511,3 @@ + } + close($fhoutLoc); + } +- +--- a/src/prof/embl/scr/lib/all5.pl ++++ b/src/prof/embl/scr/lib/all5.pl +@@ -377,7 +377,7 @@ + @tmp=split(/[\s\t]+/,$_); foreach $tmp (@tmp){$tmp=~s/\s//g;} + + if ($itrow==1){ # only first time: check numbers passed +- @colNumLoc=(1..$#tmp) if (! defined @colNumLoc || ! @colNumLoc); } ++ @colNumLoc=(1..$#tmp) if (! @colNumLoc || ! @colNumLoc); } + + # read columns + foreach $itcol (@colNumLoc) { +--- a/src/prof/embl/scr/lib/br.pl ++++ b/src/prof/embl/scr/lib/br.pl +@@ -1770,7 +1770,7 @@ + #------------------------------------------------------------------------------- + $sbrName="lib-br:"."phdHtmGetBest";$fhinLoc="FHIN_"."phdHtmGetBest"; + # check arguments +- return(&errSbr("no input!")) if (! defined @tmp || $#tmp==0); ++ return(&errSbr("no input!")) if (! @tmp || $#tmp==0); + $minLenLoc=18 if ($minLenLoc == 0); + + $max=0; +@@ -4438,17 +4438,17 @@ + # in GLOBAL: @NUM, @SEQ, @SEC(HE ), @ACC, @RISEC, @RIACC + # out: 1 if ok + #---------------------------------------------------------------------- +- if (! defined @NUM || $#NUM == 0 || ! defined @SEQ || $#SEQ == 0 || +- ! defined @SEC || $#SEC == 0 || ! defined @ACC || $#ACC == 0 || +- ! defined @RISEC || $#RISEC == 0 || +- ! defined @RIACC || $#RIACC == 0 ) { ++ if (! @NUM || $#NUM == 0 || ! @SEQ || $#SEQ == 0 || ++ ! @SEC || $#SEC == 0 || ! @ACC || $#ACC == 0 || ++ ! @RISEC || $#RISEC == 0 || ++ ! @RIACC || $#RIACC == 0 ) { + print "*** ERROR in wrt_dssp_phd: not all arguments defined!!\n"; +- print "*** missing NUM\n" if (! defined @NUM || $#NUM == 0); +- print "*** missing SEQ\n" if (! defined @SEQ || $#SEQ == 0 ); +- print "*** missing SEC\n" if (! defined @SEC || $#SEC == 0); +- print "*** missing ACC\n" if (! defined @ACC || $#ACC == 0); +- print "*** missing RISEC\n" if (! defined @RISEC || $#RISEC == 0); +- print "*** missing RIACC\n" if (! defined @RIACC || $#RIACC == 0); ++ print "*** missing NUM\n" if (! @NUM || $#NUM == 0); ++ print "*** missing SEQ\n" if (! @SEQ || $#SEQ == 0 ); ++ print "*** missing SEC\n" if (! @SEC || $#SEC == 0); ++ print "*** missing ACC\n" if (! @ACC || $#ACC == 0); ++ print "*** missing RISEC\n" if (! @RISEC || $#RISEC == 0); ++ print "*** missing RIACC\n" if (! @RIACC || $#RIACC == 0); + return(0);} + + print $fhoutLoc +--- a/src/prof/embl/scr/lib/file.pl ++++ b/src/prof/embl/scr/lib/file.pl +@@ -244,7 +244,7 @@ + $sbrName="lib-br:"."fileListWrt";$fhoutLoc="FHOUT_"."fileListWrt"; + # check arguments + return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc); +- return(0,"*** $sbrName: not def \@list!") if (! defined @listLoc || ! @listLoc); ++ return(0,"*** $sbrName: not def \@list!") if (! @listLoc || ! @listLoc); + $#tmp=0; # ------------------------------ + foreach $file (@listLoc){ # check existence + if (-e $file) { +@@ -254,7 +254,7 @@ + else { print $fhErrSbr "-*- WARN $sbrName missing file=$file,\n";}} + @listLoc=@tmp; + +- return(0,"*** $sbrName: after check none in\@list!") if (! defined @listLoc || ! @listLoc); ++ return(0,"*** $sbrName: after check none in\@list!") if (! @listLoc || ! @listLoc); + # open file + &open_file("$fhoutLoc",">$fileOutLoc") || + return(0,"*** ERROR $sbrName: fileNew=$fileOutLoc, not created\n",0); +@@ -1019,7 +1019,7 @@ + # EXA: 1 MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ + # EXA: 51 QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC + #-------------------------------------------------------------------------------- +- return(0) if (! defined @tmp || ! $#tmp); ++ return(0) if (! @tmp || ! $#tmp); + $ctLocFlag=$already_sequence=0; + foreach $tmp (@tmp){ + last if ($tmp=~/^\#/); # avoid being too friendly to GCG! +--- a/src/prof/embl/scr/lib/formats.pl ++++ b/src/prof/embl/scr/lib/formats.pl +@@ -2472,7 +2472,7 @@ + $#dir2=$Lok=0; + return(0,"no input file") if (! defined $fileInLoc); + $chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g; +- $#dir=0 if (! defined @dir); ++ $#dir=0 if (! @dir); + $Lscreen=0 if (! defined $Lscreen); + if (-d $Lscreen) { + @dir=($Lscreen,@dir); +@@ -3808,7 +3808,7 @@ + open("$fhout",">$fileOutLoc") || + return(0,"*** $sbrName cannot open fileOutLoc=$fileOutLoc\n"); + # avoid warning +- $#NUM=0 if (! defined @NUM); ++ $#NUM=0 if (! @NUM); + + # ------------------------------ + if ($Levalsec){ # write PP2dotpred format +@@ -6056,7 +6056,7 @@ + # out: $file (id or 0 for error) + #-------------------------------------------------------------------------------- + return($idLoc) if (-e $idLoc); # already existing directory +- $#dirLoc=0 if (! defined @dirLoc); ++ $#dirLoc=0 if (! @dirLoc); + if (! defined $LscreenLoc){ + $LscreenLoc=0;} + elsif (-d $Lscreen) { +--- a/src/prof/embl/scr/lib/hssp.pl ++++ b/src/prof/embl/scr/lib/hssp.pl +@@ -718,7 +718,7 @@ + # check arguments + return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc); + return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc); +- return(0,"*** $sbrName: not def \@takeLoc!") if (! defined @takeLoc || $#takeLoc<1); ++ return(0,"*** $sbrName: not def \@takeLoc!") if (! @takeLoc || $#takeLoc<1); + return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc); + # open files + &open_file("$fhinLoc","$fileInLoc") || +@@ -1062,7 +1062,7 @@ + $#dir2=$Lok=0; + return(0,"no input file") if (! defined $fileInLoc); + $chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g; +- $#dir=0 if (! defined @dir); ++ $#dir=0 if (! @dir); + $Lscreen=0 if (! defined $Lscreen); + if (-d $Lscreen) { + @dir=($Lscreen,@dir); +@@ -1205,7 +1205,7 @@ + # of all numbers wanted (i.e. = $want[M]) + undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around! + +- $#want=0 if (! defined @want); ++ $#want=0 if (! @want); + $LreadAll=0; + # ------------------------------ + # digest input +@@ -1260,7 +1260,7 @@ + # sort the array + @wantNum= sort bynumber (@wantNum); + # too many wanted +- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ ++ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ + $#tmp=0; + foreach $want (@wantNum){ + if ($want <= $locNum[$#locNum]){ +@@ -1817,7 +1817,7 @@ + $ifirLoc=0 if (! defined $ifirLoc || ($ifirLoc eq "*") ); + $ilasLoc=0 if (! defined $ilasLoc || ($ilasLoc eq "*") ); + $chainLoc=0 if (! defined $chainLoc || ($chainLoc eq "*") ); +- $#kwdRd=0 if (! defined @kwdRd); ++ $#kwdRd=0 if (! @kwdRd); + undef %tmp; + if ($#kwdRd>0){ + foreach $tmp(@kwdRd){ +--- a/src/prof/embl/scr/lib/scr.pl ++++ b/src/prof/embl/scr/lib/scr.pl +@@ -884,7 +884,7 @@ + $par{$kwd}=$par{"dirOut"}.$par{$kwd} if (-d $par{"dirOut"});}} + # ------------------------------ + # push array of output files +- $#fileOut=0 if (! defined @fileOut); ++ $#fileOut=0 if (! @fileOut); + foreach $kwd (@kwdFileOut){ + push(@fileOut,$par{$kwd});} + # ------------------------------ +@@ -1013,7 +1013,7 @@ + printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}} + # ------------------------------ + # input files +- if (defined @fileIn && $#fileIn>1){ ++ if (@fileIn && $#fileIn>1){ + # get dirs + $#tmpdir=0; + undef %tmpdir; +@@ -1036,10 +1036,10 @@ + $tmp=$fileIn[$it2]; $tmp=~s/^.*\///g; + printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;} + print $fhTraceLocSbr "\n";}} +- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ ++ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ + $tmp=0; + $tmp=$fileIn if (defined $fileIn && $fileIn); +- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1); ++ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1); + print $fhTraceLocSbr "--- \n"; + printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;} + print $fhTraceLocSbr "--- \n"; +@@ -1463,7 +1463,7 @@ + # ------------------------------ + # (1) find in arguments passed + # ------------------------------ +- if (defined @argLoc && $#argLoc > 0) { ++ if (@argLoc && $#argLoc > 0) { + foreach $arg (@argLoc) { + if ($arg=~/^ARCH=(\S+)/i) { + $archFound=$1; +@@ -1708,7 +1708,7 @@ + # check arguments + return(&errSbr("not def nperlineLoc!")) if (! defined $nperlineLoc); + return(&errSbr("not def LnumLoc!")) if (! defined $LnumLoc); +- return(&errSbr("not def ARRAYtmpLoc!")) if (! defined @tmpLoc); ++ return(&errSbr("not def ARRAYtmpLoc!")) if (! @tmpLoc); + return(&errSbr("empty ARRAYtmpLoc!")) if (! $#tmpLoc); + # return(&errSbr("not def !")) if (! defined $); + +--- a/src/prof/embl/scr/pack/copf.pm ++++ b/src/prof/embl/scr/pack/copf.pm +@@ -1847,7 +1847,7 @@ + $par{$kwd}=$par{"dirOut"}.$par{$kwd} if (-d $par{"dirOut"});}} + # ------------------------------ + # push array of output files +- $#fileOut=0 if (! defined @fileOut); ++ $#fileOut=0 if (! @fileOut); + foreach $kwd (@kwdFileOut){ + push(@fileOut,$par{$kwd});} + # ------------------------------ +@@ -1973,7 +1973,7 @@ + printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}} + # ------------------------------ + # input files +- if (defined @fileIn && $#fileIn>1){ ++ if (@fileIn && $#fileIn>1){ + # get dirs + $#tmpdir=0; undef %tmpdir; + foreach $file (@fileIn){ +@@ -1995,10 +1995,10 @@ + $tmp=$fileIn[$it2]; $tmp=~s/^.*\///g; + printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;} + print $fhTraceLocSbr "\n";}} +- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ ++ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ + $tmp=0; + $tmp=$fileIn if (defined $fileIn && $fileIn); +- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1); ++ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1); + print $fhTraceLocSbr "--- \n"; + printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;} + print $fhTraceLocSbr "--- \n"; +@@ -4441,7 +4441,7 @@ + # ------------------------------ + # (1) find in arguments passed + # ------------------------------ +- if (defined @argLoc && $#argLoc > 0) { ++ if (@argLoc && $#argLoc > 0) { + foreach $arg (@argLoc) { + if ($arg=~/^ARCH=(\S+)/i) { + $archFound=$1; +@@ -4726,7 +4726,7 @@ + # of all numbers wanted (i.e. = $want[M]) + undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around! + +- $#want=0 if (! defined @want); ++ $#want=0 if (! @want); + $LreadAll=0; + # ------------------------------ + # digest input +@@ -4779,7 +4779,7 @@ + # sort the array + @wantNum= sort bynumber (@wantNum); + # too many wanted +- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ ++ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ + $#tmp=0; + foreach $want (@wantNum){ + if ($want <= $locNum[$#locNum]){ +--- a/src/prof/embl/scr/pack/hssp_filter.pm ++++ b/src/prof/embl/scr/pack/hssp_filter.pm +@@ -1324,7 +1324,7 @@ + $par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"} if (-d $par{"dirOut"});}} + # ------------------------------ + # push array of output files +- $#fileOut=0 if (! defined @fileOut); ++ $#fileOut=0 if (! @fileOut); + foreach $kwd (@kwdFileOut){ + push(@fileOut,$par{"$kwd"});} + # ------------------------------ +@@ -1450,7 +1450,7 @@ + printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{"$kwd"};}} + # ------------------------------ + # input files +- if (defined @fileIn && $#fileIn>1){ ++ if (@fileIn && $#fileIn>1){ + # get dirs + $#tmpdir=0; undef %tmpdir; + foreach $file (@fileIn){ +@@ -1472,10 +1472,10 @@ + $tmp=$fileIn[$it2]; $tmp=~s/^.*\///g; + printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;} + print $fhTraceLocSbr "\n";}} +- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ ++ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ + $tmp=0; + $tmp=$fileIn if (defined $fileIn && $fileIn); +- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1); ++ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1); + print $fhTraceLocSbr "--- \n"; + printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;} + print $fhTraceLocSbr "--- \n"; +@@ -1700,7 +1700,7 @@ + # ------------------------------ + # (1) find in arguments passed + # ------------------------------ +- if (defined @argLoc && $#argLoc > 0) { ++ if (@argLoc && $#argLoc > 0) { + foreach $arg (@argLoc) { + if ($arg=~/^ARCH=(\S+)/i) { + $archFound=$1; +@@ -2193,7 +2193,7 @@ + # check arguments + return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc); + return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc); +- return(0,"*** $sbrName: not def \@takeLoc!") if (! defined @takeLoc || $#takeLoc<1); ++ return(0,"*** $sbrName: not def \@takeLoc!") if (! @takeLoc || $#takeLoc<1); + return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc); + # open files + &open_file("$fhinLoc","$fileInLoc") || +@@ -2246,7 +2246,7 @@ + $#dir2=$Lok=0; + return(0,"no input file") if (! defined $fileInLoc); + $chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g; +- $#dir=0 if (! defined @dir); ++ $#dir=0 if (! @dir); + $Lscreen=0 if (! defined $Lscreen); + # passed dir instead of Lscreen + if (-d $Lscreen) { @dir=($Lscreen,@dir); +--- a/src/prof/scr/conv_prof2hssp.pl ++++ b/src/prof/scr/conv_prof2hssp.pl +@@ -310,7 +310,7 @@ + $par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"};}}}} + # ------------------------------ + # push array of output files +- if (! defined @fileOut){$#fileOut=0;} ++ if (! @fileOut){$#fileOut=0;} + foreach $kwd (@kwdDef){ + if ($kwd=~/^fileOut/){ + push(@fileOut,$par{"$kwd"});}} +@@ -327,7 +327,7 @@ + $par{"$kwd"}=$par{"dirWork"}.$par{"$kwd"};}}}} + # ------------------------------ + # array of Work files +- if (! defined @fileWork){$#fileWork=0;} ++ if (! @fileWork){$#fileWork=0;} + foreach $kwd (@kwdDef){ + if (($kwd=~/^file/)&&($kwd!~/^fileIn/)&&($kwd!~/^fileOut/)){ + push(@fileWork,$par{"$kwd"});}} +@@ -511,4 +511,3 @@ + } + close($fhoutLoc); + } +- +--- a/src/prof/scr/lib/dead_code.pl ++++ b/src/prof/scr/lib/dead_code.pl +@@ -15,7 +15,7 @@ + #------------------------------------------------------------------------------- + $SBR4=""."nnJury"; $fhinLoc="FHIN_"."nnJury";$fhoutLoc="FHOUT_"."nnJury"; + # check arguments +- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc || ++ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc || + ! @fileOutNetLoc); + # -------------------------------------------------- + # loop over all output files +@@ -1338,4 +1338,3 @@ + print $FHTRACE $tmpWrt; } + return($itVec); + } # end of assVec_strLocRel +- +--- a/src/prof/scr/lib/lib-col.pl ++++ b/src/prof/scr/lib/lib-col.pl +@@ -652,7 +652,7 @@ + } + # ------------------------------ + # push array of output files +- $#fileOut=0 if (! defined @fileOut); ++ $#fileOut=0 if (! @fileOut); + foreach $kwd (@kwdFileOut){ + push(@fileOut,$par{$kwd});} + # ------------------------------ +@@ -773,7 +773,7 @@ + printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}} + # ------------------------------ + # input files +- if (defined @fileIn && $#fileIn>1){ ++ if (@fileIn && $#fileIn>1){ + # get dirs + $#tmpdir=0; + undef %tmpdir; +@@ -796,10 +796,10 @@ + $tmp=$fileIn[$it2]; $tmp=~s/^.*\///g; + printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;} + print $fhTraceLocSbr "\n";}} +- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ ++ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ + $tmp=0; + $tmp=$fileIn if (defined $fileIn && $fileIn); +- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1); ++ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1); + print $fhTraceLocSbr "--- \n"; + printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;} + print $fhTraceLocSbr "--- \n"; +@@ -2320,7 +2320,7 @@ + # EXA: 1 MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ + # EXA: 51 QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC + #-------------------------------------------------------------------------------- +- return(0) if (! defined @tmp || ! $#tmp); ++ return(0) if (! @tmp || ! $#tmp); + $ctLocFlag=$already_sequence=0; + foreach $tmp (@tmp){ + last if ($tmp=~/^\#/); # avoid being too friendly to GCG! +@@ -2752,7 +2752,7 @@ + # in: @tmp: + # out: 1 if is yes; 0 else + #-------------------------------------------------------------------------------- +- return(0) if (! defined @tmp || ! $#tmp); ++ return(0) if (! @tmp || ! $#tmp); + foreach $tmp (@tmp){ + return(0) if ($tmp=~/[^A-Z.~_![:space:]]/i); + } +--- a/src/prof/scr/lib/lib-prof.pl ++++ b/src/prof/scr/lib/lib-prof.pl +@@ -426,7 +426,7 @@ + return(&errSbr("missing par{extBlastMat}!", $SBR6)) if (! defined $par{"extBlastMat"} || + length($par{"extBlastMat"}) < 3); + return(&errSbr("missing Hash_ARRAYhssp!", $SBR6)) if (! %hssp); +- return(&errSbr("missing Norm_ARRAYaa!", $SBR6)) if (! defined @aa || ! @aa); ++ return(&errSbr("missing Norm_ARRAYaa!", $SBR6)) if (! @aa || ! @aa); + + + +@@ -2820,7 +2820,7 @@ + return(&errSbr("not def acc3Thresh1!",$SBR6),0) if (! defined $acc3Thresh1); + return(&errSbr("not def acc3Thresh2!",$SBR6),0) if (! defined $acc3Thresh2); + return(&errSbr("bitaccLoc < 1!",$SBR6),0) if ($bitaccLoc<1); +- return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! defined @vecLoc || $#vecLoc<1); ++ return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! @vecLoc || $#vecLoc<1); + + $undecidedLoc=$bitaccLoc*0.5 if (! defined $undecidedLoc); + +@@ -2884,7 +2884,7 @@ + # check arguments + return(&errSbr("not def accRelLoc!", $SBR6),0) if (! defined $accRelLoc); + return(&errSbr("not def acc2Thresh!", $SBR6),0) if (! defined $acc2Thresh); +- return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! defined @prdLoc || $#prdLoc<1); ++ return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! @prdLoc || $#prdLoc<1); + + # ------------------------------ + # fast end for others +@@ -2944,7 +2944,7 @@ + return(&errSbr("not def accRelLoc!", $SBR6),0) if (! defined $accRelLoc); + return(&errSbr("not def acc3Thresh1!",$SBR6),0) if (! defined $acc3Thresh1); + return(&errSbr("not def acc3Thresh2!",$SBR6),0) if (! defined $acc3Thresh2); +- return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! defined @prdLoc || $#prdLoc<1); ++ return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! @prdLoc || $#prdLoc<1); + + # ------------------------------ + # compile averages over each state +@@ -3002,7 +3002,7 @@ + # check arguments + return(&errSbr("not def modepredLoc!",$SBR6),0) if (! defined $modepredLoc); + return(&errSbr("not def posWinLoc!",$SBR6),0) if (! defined $posWinLoc); +- return(&errSbr("not def outnum2symLoc!",$SBR6),0) if (! defined @outnum2symLoc || ++ return(&errSbr("not def outnum2symLoc!",$SBR6),0) if (! @outnum2symLoc || + $#outnum2symLoc<1); + return(&errSbr("numout must be > 1, here",$SBR6),0) if ($#outnum2symLoc<2); + return(&errSbr("undefined symbol for posWinLoc=$posWinLoc, outnum2symLoc=". +@@ -3055,7 +3055,7 @@ + return(&errSbr("not def modepredLoc!",$SBR6),0) if (! defined $modepredLoc); + return(&errSbr("not def bitaccLoc!",$SBR6),0) if (! defined $bitaccLoc); + return(&errSbr("bitaccLoc < 1!",$SBR6),0) if ($bitaccLoc<1); +- return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! defined @vecLoc || $#vecLoc<1); ++ return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! @vecLoc || $#vecLoc<1); + # -------------------------------------------------- + # distinguish prediction modes + # -------------------------------------------------- +@@ -5309,7 +5309,7 @@ + + # ------------------------------ + # symbols for output units +- if (! defined @outnum2sym || ! $#outnum2sym){ ++ if (! @outnum2sym || ! $#outnum2sym){ + foreach $itout (1..$numoutLoc){ + push(@outnum2sym,$ptrGlob{"outnum2sym",$itout}); + }} +@@ -6073,7 +6073,7 @@ + $SBR4=""."nn3rdProcessOnesam"; + # check arguments + return(&errSbr("not def modepredLoc!",$SBR4)) if (! defined $modepredLoc); +- return(&errSbr("not def outputs!",$SBR4)) if (! defined @tmp); ++ return(&errSbr("not def outputs!",$SBR4)) if (! @tmp); + + $#out=$sum=0; + foreach $itout (1..$#tmp){ +@@ -6734,7 +6734,7 @@ + $LverbLoc=0; # temporary writes + # $LverbLoc=1; + # check arguments +- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc || ++ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc || + ! @fileOutNetLoc); + + @winoutJoinLoc=split(/,/,$winoutJoinLoc); +@@ -6991,7 +6991,7 @@ + #------------------------------------------------------------------------------- + $SBR4=""."nnJurySpecial"; $fhinLoc="FHIN_"."nnJurySpecial";$fhoutLoc="FHOUT_"."nnJurySpecial"; + # check arguments +- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc || ++ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc || + ! @fileOutNetLoc); + # -------------------------------------------------- + # loop over all output files +@@ -7118,7 +7118,7 @@ + #------------------------------------------------------------------------------- + $SBR4=""."nnJuryWeight"; $fhinLoc="FHIN_"."nnJuryWeight";$fhoutLoc="FHOUT_"."nnJuryWeight"; + # check arguments +- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc || ++ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc || + ! @fileOutNetLoc); + @winoutJoinLoc=split(/,/,$winoutJoinLoc); + +@@ -8099,7 +8099,7 @@ + # out GLOBAL: @codeUnitIn1st + # out GLOBAL: @num_codeUnitIn (if $Ldobuild2nd) + # -------------------------------------------------- +- if (! defined @codeUnitIn1st) { ++ if (! @codeUnitIn1st) { + ($Lok,$msg)= + &decode_inputUnits1st($winHalf,$modeinLoc,$numaaLoc + ); return(&errSbrMsg("spoiled decode_inputUnits1st(1)", +@@ -8631,7 +8631,7 @@ + + # ------------------------------ + # add additional local information: go through window +- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ ++ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ + foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){ + foreach $scale (@hydrophobicityScalesWanted) { + push(@vecIn,$prot{$itwin,$scale}); +@@ -8641,7 +8641,7 @@ + # local info: once per window + + # sum over hydrophobicity (i+2,+3,+4) +- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ ++ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ + foreach $scale (@hydrophobicityScalesWantedSum) { + push(@vecIn,split(/,/,$prot{$itres,$scale."sum",($winHalf*2+1)})); + }} +@@ -8730,7 +8730,7 @@ + + # ------------------------------ + # add additional local information: go through window +- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ ++ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ + foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){ + foreach $scale (@hydrophobicityScalesWanted) { + push(@vecIn,$prot{$itwin,$scale}); +@@ -8740,7 +8740,7 @@ + # local info: once per window + + # sum over hydrophobicity (i+2,+3,+4) +- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ ++ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ + foreach $scale (@hydrophobicityScalesWantedSum) { + push(@vecIn,split(/,/,$prot{$itres,$scale."sum",($winHalf*2+1)})); + }} +@@ -8858,7 +8858,7 @@ + + # ------------------------------ + # add additional local information: go through window +- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ ++ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ + foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){ + foreach $scale (@hydrophobicityScalesWanted) { + if (defined $prot_hydro{$itwin,$scale}){ +@@ -8871,7 +8871,7 @@ + # local info: once per window + + # sum over hydrophobicity (i+2,+3,+4) +- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ ++ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ + foreach $scale (@hydrophobicityScalesWantedSum) { + if (defined $prot_hydro{$itres,$scale."sum",($winHalf*2+1)}){ + push(@vecIn,split(/,/,$prot_hydro{$itres,$scale."sum",($winHalf*2+1)}));} +@@ -8943,7 +8943,7 @@ + + # ------------------------------ + # add additional local information: go through window +- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ ++ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){ + $#tmp=0; + foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){ + foreach $scale (@hydrophobicityScalesWanted) { +@@ -8957,7 +8957,7 @@ + # ------------------------------ + # local info: once per window + # sum over hydrophobicity (i+2,+3,+4) +- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ ++ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){ + $#tmp=0; + foreach $scale (@hydrophobicityScalesWantedSum) { + if (defined $prot_hydro{$itres,$scale."sum",($winHalf*2+1)}){ +@@ -9572,7 +9572,7 @@ + #------------------------------------------------------------------------------- + $sbrName="lib-br:"."phdHtmGetBest";$fhinLoc="FHIN_"."phdHtmGetBest"; + # check arguments +- return(&errSbr("no input!")) if (! defined @tmp || $#tmp==0); ++ return(&errSbr("no input!")) if (! @tmp || $#tmp==0); + $minLenLoc=18 if ($minLenLoc == 0); + + $max=0; Added: trunk/packages/rostlab/profphd/trunk/debian/patches/2_remove_perlbrew_usage.patch =================================================================== --- trunk/packages/rostlab/profphd/trunk/debian/patches/2_remove_perlbrew_usage.patch (rev 0) +++ trunk/packages/rostlab/profphd/trunk/debian/patches/2_remove_perlbrew_usage.patch 2016-08-24 13:37:16 UTC (rev 22713) @@ -0,0 +1,15 @@ +Author: Tatiana Malygina <[email protected]> +Description: remove perlbrew to use latest perl 5.22 +Last-Update: 2016-08-23 + +--- a/src/prof/prof ++++ b/src/prof/prof +@@ -35,7 +35,7 @@ + echoerr "" + } + +-if [ ${PERL_VER} -ge ${PERL_BAD} ] ++if [ ${PERL_VER} -le ${PERL_BAD} ] + then + ## Do stuff with perl 5.10.1 if perlbrew installed + if [ -x ${PERLBREW_PATH} ] Added: trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch =================================================================== --- trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch (rev 0) +++ trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch 2016-08-24 13:37:16 UTC (rev 22713) @@ -0,0 +1,27 @@ +Author: Tatiana Malygina <[email protected]> +Description: fix error "Modification of non-creatable array value attempted, + subscript -1 at /usr/share/profphd/prof/scr/lib/lib-prof.pl line 7739" +Last-Update: 2016-08-23 + +--- a/src/prof/scr/lib/lib-prof.pl ++++ b/src/prof/scr/lib/lib-prof.pl +@@ -7736,7 +7737,7 @@ + ++$tmplen[$cth];} + } + # set last +- $tmpend[$cth]=$tmplen[$cth] if (! defined $tmpend[$cth]); ++ $tmpend[$cth]=$tmplen[$cth] if (! defined $tmpend[$cth] && $cth >= $[ ); + # -------------------------------------------------- + # find short ones + foreach $it (1..$#tmpbeg){ +@@ -7847,8 +7848,8 @@ + else { + ++$tmplen[$cte];} + } +- # set last +- $tmpend[$cte]=$tmplen[$cte] if (! defined $tmpend[$cte]); ++ # set last ++ $tmpend[$cte]=$tmplen[$cte] if (! defined $tmpend[$cte] && $cte >= $[ ); + # -------------------------------------------------- + # find short ones + foreach $it (1..$#tmpbeg){ Added: trunk/packages/rostlab/profphd/trunk/debian/patches/4_fix_negative_repeat_count.patch =================================================================== --- trunk/packages/rostlab/profphd/trunk/debian/patches/4_fix_negative_repeat_count.patch (rev 0) +++ trunk/packages/rostlab/profphd/trunk/debian/patches/4_fix_negative_repeat_count.patch 2016-08-24 13:37:16 UTC (rev 22713) @@ -0,0 +1,233 @@ +Author: Tatiana Malygina <[email protected]> +Description: fix error "Negative repeat count does nothing at" for various + lines (including possible places where this error might appear - + by semi-autoreplacement) +Last-Update: 2016-08-24 + +--- a/src/prof/scr/lib/lib-prof.pl ++++ b/src/prof/scr/lib/lib-prof.pl +@@ -1,5 +1,6 @@ + #use Data::Dumper; + use Carp qw| cluck :DEFAULT |; ++use List::Util qw[max]; + no warnings 'deprecated'; + #------------------------------------------------------------------------------# + # Copyright Sep, 1998 # +@@ -4401,7 +4402,7 @@ + # loop over all alis + foreach $itAli (@wantNum){ + $hssp{"fin",$itAli}.=$hssp{"ali",$itAli,$itRes}; +- $hssp{"fin",$itAli}.="." x (1 + $insMax - length($hssp{"ali",$itAli,$itRes})); ++ $hssp{"fin",$itAli}.="." x max(1 + $insMax - length($hssp{"ali",$itAli,$itRes}), 0); + } + } + # ------------------------------ +@@ -11580,7 +11581,7 @@ + next if ($rdb{$kwd}=~/^\s*$/); + $tmp{$kwd}=1; + $tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/; +- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$rdb{$kwd}); ++ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$rdb{$kwd}); + + # other info + if ($kwd =~ /prot_nfar/ && $#otherDistance){ +@@ -11595,7 +11596,7 @@ + $val= $rdb{$kwd,$other}; + $kwd2=$kwd.$other;} + $tmp=$kwd2; $tmp=~tr/[a-z]/[A-Z]/; +- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$val); ++ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$val); + }} + } + +@@ -11618,7 +11619,7 @@ + next if ($rdb{$kwd}=~/^\s*$/); + $tmp{$kwd}=1; + $tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/; +- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$rdb{$kwd});} ++ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$rdb{$kwd});} + push(@tmpwrt,@tmp2,"# ") if ($#tmp2 > 3); + + # ------------------------------ +@@ -11634,7 +11635,7 @@ + @tmpval=split(/\t/,$rdb{$kwd}); + $tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/; + foreach $tmpval (@tmpval){ +- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhiteHtm-length($tmp)) .": ".$tmpval); ++ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhiteHtm-length($tmp), 0) .": ".$tmpval); + } + } + push(@tmpwrt,@tmp2,"# ") if ($#tmp2>3); +@@ -11649,7 +11650,7 @@ + next if ($rdb{$kwd}=~/^\s*$/); + $tmp{$kwd}=1; + $tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/; +- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$rdb{$kwd});} ++ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$rdb{$kwd});} + if ($#tmp2>3) { push(@tmpwrt,@tmp2,"# "); + $Lnet=1;} else {$Lnet=0;} + +@@ -11830,12 +11831,12 @@ + + # ------------------------------ + # notation: header: protein +- $tmp="HEADER". " " x ($numwhite-6) . ": PROTEIN"; ++ $tmp="HEADER". " " x max($numwhite-6, 0) . ": PROTEIN"; + push(@tmp2, + "# ", + # "# NOTATION "."-" x length($tmp), + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) + ); + foreach $kwd ("prot_id","prot_name","prot_nres","prot_nchn","prot_kchn", + "prot_nali","prot_nfar"){ +@@ -11843,60 +11844,60 @@ + next if (! defined $tmp{$kwd}); + $tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/; + $tmpcontd=$kwd." contd"; +- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": "; +- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": "; ++ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": "; ++ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": "; + $notation=$par{"notation",$kwd}; + $notation=~s/\n/\n$tmpdescontd/g; + push(@tmp2,$tmpdes.$notation);} + + # ------------------------------ + # notation: header: alignment +- $tmp="HEADER". " " x ($numwhite-6) . ": ALIGNMENT"; ++ $tmp="HEADER". " " x max($numwhite-6, 0) . ": ALIGNMENT"; + push(@tmp2, + "# ", + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp))); ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0)); + foreach $kwd ("ali_orig","ali_used","ali_para" + ){ + next if (! defined $par{"notation",$kwd}); + next if (! defined $tmp{$kwd}); + $tmpcontd=$kwd." contd"; +- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": "; +- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": "; ++ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": "; ++ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": "; + $notation=$par{"notation",$kwd}; + $notation=~s/\n/\n$tmpdescontd/g; + push(@tmp2,$tmpdes.$notation);} + + # ------------------------------ + # notation: header: network +- $tmp="HEADER". " " x ($numwhite-6) . ": INTERNAL"; ++ $tmp="HEADER". " " x max($numwhite-6, 0) . ": INTERNAL"; + push(@tmp2, + "# ", + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp))); ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0)); + foreach $kwd ("prof_fpar","prof_nnet","prof_fnet","prof_mode"){ + next if (! defined $par{"notation",$kwd}); + next if (! defined $tmp{$kwd}); + $tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/; + $tmpcontd=$kwd." contd"; +- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": "; +- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": "; ++ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": "; ++ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": "; + $notation=$par{"notation",$kwd}; + push(@tmp2,$tmpdes.$notation);} + + # ------------------------------ + # notation: body: protein + push(@tmp2,"# "); +- $tmp="BODY ". " " x ($numwhite-5) . ": PROTEIN"; ++ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROTEIN"; + push(@tmp2, + "# ", + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp))); ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0)); + foreach $kwd ("No","AA","CHN"){ + next if (! defined $par{"notation",$kwd}); + $tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/; +- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": "; +- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": "; ++ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": "; ++ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": "; + $notation=$par{"notation",$kwd}; + $notation=~s/\n/\n$tmpdescontd/g; + push(@tmp2,$tmpdes.$notation);} +@@ -11906,11 +11907,11 @@ + + $#tmp=0; + if ($whichPROFloc =~ /^(3|both)$/){ +- $tmp="BODY ". " " x ($numwhite-5) . ": PROF"; ++ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROF"; + push(@tmp, + "# ", + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));} ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));} + else { + push(@tmp, + "# ");} +@@ -11950,7 +11951,7 @@ + $tmp=$kwd; + # $tmp=~tr/[a-z]/[A-Z]/; + # split annotations too long +- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": "; ++ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": "; + $notation=$par{"notation",$kwd}; + # no new line in RDB + $notation=~s/\n/ /g; +@@ -11958,22 +11959,22 @@ + # insert header + if ($kwd =~ /ACC/ && ! defined $tmp{"acc"}){ + $tmp{"acc"}=1; +- $tmp="BODY ". " " x ($numwhite-5) . ": PROFacc"; ++ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROFacc"; + push(@tmp,"# ", + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));} ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));} + elsif ($kwd =~ /HEL/ && ! defined $tmp{"sec"}){ + $tmp{"sec"}=1; +- $tmp="BODY ". " " x ($numwhite-5) . ": PROFsec"; ++ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROFsec"; + push(@tmp,"# ", + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));} ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));} + elsif ($kwd =~ /MN/ && ! defined $tmp{"htm"}){ + $tmp{"htm"}=1; +- $tmp="BODY ". " " x ($numwhite-5) . ": PROFhtm"; ++ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROFhtm"; + push(@tmp,"# ", + "# "."-" x 72, +- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));} ++ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));} + + # ------------------------------ + # add to final +@@ -11984,7 +11985,7 @@ + if (defined $PROF_SKIP){ + $tmp="NOTE"; + push(@tmp, +- "# NOTATION ".$tmp." " x ($numwhite-length($tmp)) .": ".$par{"notation","prof_skip"});} ++ "# NOTATION ".$tmp." " x max($numwhite-length($tmp), 0) .": ".$par{"notation","prof_skip"});} + push(@tmp2, + @tmp, + "# " , +@@ -12048,10 +12049,10 @@ + $white="10"; + print + # "--- ------------------------------------------------------------------\n", +- "--- PROF: ",$dateLoc, " " x ($white-length($dateLoc)), ++ "--- PROF: ",$dateLoc, " " x max($white-length($dateLoc), 0), + " run time=",&fctRunTime($timeBegLoc),"\n"; + print +- "--- N proteins: ",$nfileInLoc," " x ($white-length($nfileInLoc)), ++ "--- N proteins: ",$nfileInLoc," " x max($white-length($nfileInLoc), 0), + " time per protein=",&fctSeconds2time((time-$timeBegLoc)/$nfileInLoc),"\n" + if ($nfileInLoc > 2); + Added: trunk/packages/rostlab/profphd/trunk/debian/patches/series =================================================================== --- trunk/packages/rostlab/profphd/trunk/debian/patches/series (rev 0) +++ trunk/packages/rostlab/profphd/trunk/debian/patches/series 2016-08-24 13:37:16 UTC (rev 22713) @@ -0,0 +1,4 @@ +1_remove_defined_array.patch +2_remove_perlbrew_usage.patch +3_fix_indexing.patch +4_fix_negative_repeat_count.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
