This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch master in repository perlprimer.
commit 90fbf5e275841dd6c9193aed16fd049cc84e8150 Author: Charles Plessy <[email protected]> Date: Sun Jan 22 17:27:40 2017 +0900 Delete patches, applied upstream. --- debian/patches/fixarray.patch | 16 ---- debian/patches/series | 3 - debian/patches/spelling.patch | 37 ---------- debian/patches/sytaxerrors.patch | 155 --------------------------------------- 4 files changed, 211 deletions(-) diff --git a/debian/patches/fixarray.patch b/debian/patches/fixarray.patch deleted file mode 100644 index a9fa4dd..0000000 --- a/debian/patches/fixarray.patch +++ /dev/null @@ -1,16 +0,0 @@ -Author: Canberk Koç <[email protected]> -Last-Update: Sat, 02 Jul 2016 20:57:19 +0000 -Bugs-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/perlprimer/+bug/1575074 -Description: Adapt to Perl 5.22 - ---- a/perlprimer.pl -+++ b/perlprimer.pl -@@ -5226,7 +5226,7 @@ sub generate_report { - } - - my ($hlist_sel) = $$hlist_ref->selectionGet; -- unless (defined(@$slist) && defined($hlist_sel)) { -+ unless (@$slist && defined($hlist_sel)) { - dialogue("The Generate Report function saves the statistics and alignment of a particular primer pair - please select a primer pair first"); - return; - } diff --git a/debian/patches/series b/debian/patches/series deleted file mode 100644 index d49e310..0000000 --- a/debian/patches/series +++ /dev/null @@ -1,3 +0,0 @@ -sytaxerrors.patch -fixarray.patch -spelling.patch diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch deleted file mode 100644 index 9f5fce3..0000000 --- a/debian/patches/spelling.patch +++ /dev/null @@ -1,37 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Sat, 2 Jul 2016 23:54:40 +0300 -Description: Fix spelling - ---- a/ReadMe -+++ b/ReadMe -@@ -28,7 +28,7 @@ Perlprimer's current features include th - * Ability to add cloning sequences to primers, automatically adjusted to be in-frame - * QPCR primer design without manual intron-exon boundary entry - --Perlprimer calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use default, standard, PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified. -+Perlprimer calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use default, standard, PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yield of product when amplified. - - Perlprimer is written in Perl and requires Perl/Tk. In addition, for QPCR functionality perlprimer requires the open-source Spidey executable from NCBI. The program is designed to be cross-platform and has been tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also had success using the program under Mac OS X. - ---- a/ReadMe.txt -+++ b/ReadMe.txt -@@ -28,7 +28,7 @@ Perlprimer's current features include th - * Ability to add cloning sequences to primers, automatically adjusted to be in-frame - * QPCR primer design without manual intron-exon boundary entry - --Perlprimer calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use default, standard, PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified. -+Perlprimer calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use default, standard, PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yield of product when amplified. - - Perlprimer is written in Perl and requires Perl/Tk. In addition, for QPCR functionality perlprimer requires the open-source Spidey executable from NCBI. The program is designed to be cross-platform and has been tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also had success using the program under Mac OS X. - ---- a/perlprimer.pl -+++ b/perlprimer.pl -@@ -3299,7 +3299,7 @@ sub primer_dimer_new { - } - } - -- # check for best binding for each possibility that yeilds two or more matched bases together -+ # check for best binding for each possibility that yields two or more matched bases together - my $last; - my @unequal_loops; - foreach my $i (@binding_data) { diff --git a/debian/patches/sytaxerrors.patch b/debian/patches/sytaxerrors.patch deleted file mode 100644 index 615bfab..0000000 --- a/debian/patches/sytaxerrors.patch +++ /dev/null @@ -1,155 +0,0 @@ -Author: Steffen Moeller <[email protected]> -Description: Fixes a series of errors indicated by Perl 5.18. -Forwarded: https://sourceforge.net/p/perlprimer/patches/6/ - ---- git.orig/perlprimer.pl -+++ git/perlprimer.pl -@@ -3093,23 +3093,24 @@ - # and because it's 3' primer-dimers that are the real problem in PCR. - - # create a binding array for each of the four bases -- for $l (0 .. $pfl-1) { -+ foreach $l (0 .. $pfl-1) { - my $mbase = substr($fprimer_r, $l, 1); - $primer_hash{$mbase}[$l]=1; -- for $k qw(a g c t) { -+ my @nucleotides = qw(a g c t); -+ foreach $k (@nucleotides) { - $primer_hash{$k}[$l] ||=0; - } - } - - # create the primer matrix - my @primer_comp; -- for $k (0 .. $prl-1) { -+ foreach $k (0 .. $prl-1) { - $primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)}; - } - - # read each combination from the matrix, calculate dG for each dimer - my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2); -- for $k (0 .. $pd_len) { -+ foreach $k (0 .. $pd_len) { - $score[$k]=0; - my $bind; - my $score_p=0; -@@ -3129,7 +3130,7 @@ - # } - - # read the binding data -- for $l (0 .. $prl-1) { -+ foreach $l (0 .. $prl-1) { - if (($k-$l)<$pfl) { - $bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0; - } else { -@@ -3148,7 +3149,7 @@ - - # Find start and end of similarity - my ($pb_init,$pb_end); -- for $l (0 .. length($bind)-1) { -+ foreach $l (0 .. length($bind)-1) { - # at first I tried finding the initiating terminal bases with - # regexps, but that was much slower ... - if (substr($bind, $l, 1) eq "1") { -@@ -3159,7 +3160,7 @@ - - if (defined($pb_init)) { - # deltaG calculation -- for $l ($pb_init .. $pb_end-1) { -+ foreach $l ($pb_init .. $pb_end-1) { - next if substr($bind, $l, 2) eq "00"; - next if substr($bind, $l, 1) eq "2"; - $score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)}; -@@ -3228,44 +3229,44 @@ - # and because it's 3' primer-dimers that are the real problem in PCR. - - # create a binding array for each of the four bases -- for $l (0 .. $pfl-1) { -+ foreach $l (0 .. $pfl-1) { - my $mbase = substr($fprimer_r, $l, 1); - $primer_hash{$mbase}[$l]=1; -- for $k qw(a g c t) { -+ foreach $k (qw(a g c t)) { - $primer_hash{$k}[$l] ||=0; - } - } - - # create the primer matrix - my @primer_comp; -- for $k (0 .. $prl-1) { -- $primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)}; -+ foreach my $kk (0 .. $prl-1) { -+ $primer_comp[$kk]=$primer_hash{substr($rcomprlc, $kk, 1)}; - } - - # print the matrix - for debugging - print "$primer_f vs. $primer_r - full pd = $pd_full\n"; - print " \t"; -- for $l (0 .. $pfl-1) { -+ foreach $l (0 .. $pfl-1) { - my $mbase = substr($fprimer_r, $l, 1); - print "$mbase "; - } - print "\n"; -- for $k (0 .. $prl-1) { -- my $base = substr($rprimer_r, $k, 1); -- print "$base:\t@{$primer_comp[$k]}\n"; -+ foreach my $kk (0 .. $prl-1) { -+ my $base = substr($rprimer_r, $kk, 1); -+ print "$base:\t@{$primer_comp[$kk]}\n"; - } - - my @binding_data; - # read each combination from the matrix, calculate dG for each dimer - my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2); -- for my $k (0 .. $pd_len) { -- $score[$k]=0; -+ foreach my $kk (0 .. $pd_len) { -+ $score[$kk]=0; - my $bind; - my $score_p=0; - - # starting coords -- my $pf_coord_start = ($k >= $pfl ? $pfl-1 : $k); -- my $pr_coord_start = ($k - $pfl > 0 ? $k - $pfl : 0); -+ my $pf_coord_start = ($kk >= $pfl ? $pfl-1 : $kk); -+ my $pr_coord_start = ($kk - $pfl > 0 ? $kk - $pfl : 0); - my ($pf_coord, $pr_coord, $first, $flag); - - # read through each combination finding multiple matches -@@ -3285,7 +3286,7 @@ - } - } elsif ($flag) { - # end of a binding stretch -- push @binding_data, [$k, $first, $bind] if $bind > 1; -+ push @binding_data, [$kk, $first, $bind] if $bind > 1; - $bind=0; - $flag=0; - } -@@ -3325,7 +3326,7 @@ - # # } - # - # # read the binding data -- # for $l (0 .. $prl-1) { -+ # foreach $l (0 .. $prl-1) { - # if (($k-$l)<$pfl) { - # $bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0; - # } else { -@@ -3344,7 +3345,7 @@ - # - # # Find start and end of similarity - # my ($pb_init,$pb_end); -- # for $l (0 .. length($bind)-1) { -+ # foreach $l (0 .. length($bind)-1) { - # # at first I tried finding the initiating terminal bases with - # # regexps, but that was much slower ... - # if (substr($bind, $l, 1) eq "1") { -@@ -3355,7 +3356,7 @@ - # - # if (defined($pb_init)) { - # # deltaG calculation -- # for $l ($pb_init .. $pb_end-1) { -+ # foreach $l ($pb_init .. $pb_end-1) { - # next if substr($bind, $l, 2) eq "00"; - # next if substr($bind, $l, 1) eq "2"; - # $score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)}; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/perlprimer.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
