[med-svn] r22713 - in trunk/packages/rostlab/profphd/trunk/debian: . patches
Tatiana Malygina
latticetower-guest at moszumanska.debian.org
Wed Aug 24 13:37:17 UTC 2016
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 <merlettaia at gmail.com> 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 <merlettaia at gmail.com>
+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, at 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, at 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, at 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, at 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, at 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, at 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 <merlettaia at gmail.com>
+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 ${PERLBREW_PATH} ]
Added: trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/patches/3_fix_indexing.patch 2016-08-24 13:37:16 UTC (rev 22713)
@@ -0,0 +1,27 @@
+Author: Tatiana Malygina <merlettaia at gmail.com>
+Description: fix error "Modification of non-creatable array value attempted,
+ subscript -1 at /usr/share/profphd/prof/scr/lib/lib-prof.pl line 7739"
+Last-Update: 2016-08-23
+
+--- a/src/prof/scr/lib/lib-prof.pl
++++ b/src/prof/scr/lib/lib-prof.pl
+@@ -7736,7 +7737,7 @@
+ ++$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 <merlettaia at gmail.com>
+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{$kwd});}
+ push(@tmpwrt, at tmp2,"# ") if ($#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) .": ".$tmpval);
+ }
+ }
+ push(@tmpwrt, at tmp2,"# ") if ($#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, at 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
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