[med-svn] [gbrowse] 01/01: add patch to fix bug #826458

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository gbrowse.

commit 4dd4fc14fcfc9eda09cbecf8834e7e793c0386f8
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Wed Dec 14 11:06:22 2016 +0100

    add patch to fix bug #826458
---
 debian/patches/fix_perl_deprecation | 18 ++++++++++++++++++
 debian/patches/series               |  1 +
 2 files changed, 19 insertions(+)

diff --git a/debian/patches/fix_perl_deprecation b/debian/patches/fix_perl_deprecation
new file mode 100644
index 0000000..9ce15af
--- /dev/null
+++ b/debian/patches/fix_perl_deprecation
@@ -0,0 +1,18 @@
+Subject: perl deprecated left brakets i nregexp without escape
+Description: warning switched to error in perl, need to escape
+ brakets in perl regexp if braket is a string pattern
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2016-12-14
+Bug: 82648
+Forwarded: no
+--- a/lib/Bio/Graphics/Browser2/DataSource.pm
++++ b/lib/Bio/Graphics/Browser2/DataSource.pm
+@@ -960,7 +960,7 @@
+ 
+   # Do environment substitutions in the args. Assume that the environment is safe.
+   foreach (@argv) {
+-      s/\$ENV{(\w+)}/$ENV{$1}||''/ge;
++      s/\$ENV\{(\w+)\}/$ENV\{$1\}||''/ge;
+       s/\$HTDOCS/Bio::Graphics::Browser2->htdocs_base/ge;
+       s/\$DB/Bio::Graphics::Browser2->db_base/ge;
+       s/\$CONF/Bio::Graphics::Browser2->config_base/ge;
diff --git a/debian/patches/series b/debian/patches/series
index 98a3845..99a42a2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ fix_pop_url
 skipRenderFarmTest_UpstreamBug12
 skip_check_installed_test.patch
 source_init_functions
+fix_perl_deprecation

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