Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko
--- a/debian/bkgd.gif
+++ b/debian/bkgd.gif
--- a/debian/changelog
+++ b/debian/changelog
-ncbi-tools6 (6.1.20170106-3) UNRELEASED; urgency=medium
+ncbi-tools6 (6.1.20170106-3) unstable; urgency=medium

  [ Liubov Chuprikova ]
-  * Team upload.
  * Added autopkgtest for ncbi-tools-bin. 
    Closes: #879619

  [ Aaron M. Ucko ]
+  * debian/{*.gif,ncbi2.css}: Add local copies of NCBI resources used by HTML
+    docs.
+  * debian/control:
+    - Repoint Vcs-* at salsa.debian.org.
+    - Standards-Version: 4.1.4 (already compliant).
+    - Rules-Requires-Root: no (confirmed safe).
+  * debian/{libncbi6,ncbi-tools-x11}.docs: Install resources from debian/ as
+    needed.
  * debian/source/format: Set to 3.0 (quilt) to accommodate binary test data.
-  * debian/source/include-binaries: List debian/tests/test-data/nc0305.aso.gz.
+  * debian/source/include-binaries: List debian/tests/test-data/nc0305.aso.gz
+    and (individually) debian/*.gif.
  * debian/source/options: single-debian-patch (tracking changes purely
    with git for now).
  * debian/source/patch-header: "Combined patches from git."
-  * demo/taxblast_main.c: Call SOCK_SetupSSL (accidentally missed earlier).
-  * make/makenet.unx: Link taxblast against $(LIBTLS) and $(GNUTLS_LIBS).
-
- -- Aaron M. Ucko <ucko@debian.org>  Thu, 12 Apr 2018 19:50:13 -0400
+  * demo/{findspl,taxblast_main}.c: Call SOCK_SetupSSL (accidentally missed
+    earlier).
+  * doc/{dispatcher,firewall}.html: Patch to use (newly supplied) local
+    resources, addressing a generic privacy breach caught by Lintian.
+  * make/make{demo,net}.unx: Link findspl and taxblast against $(LIBTLS)
+    and $(GNUTLS_LIBS).
+
+ -- Aaron M. Ucko <ucko@debian.org>  Sun, 24 Jun 2018 12:06:15 -0400

 ncbi-tools6 (6.1.20170106-2) unstable; urgency=medium


--- a/debian/control
+++ b/debian/control
@@ -13,10 +13,11 @@ Build-Depends-Arch: csh | c-shell,
               libpcre3-dev,
               libpng-dev,
               libxmu-dev
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ncbi-tools6.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/ncbi-tools6.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/ncbi-tools6
+Vcs-Git: https://salsa.debian.org/med-team/ncbi-tools6.git
 Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/
+Rules-Requires-Root: no

 Package: libncbi6
 Architecture: any

--- a/debian/left.gif
+++ b/debian/left.gif
--- a/debian/libncbi6.docs
+++ b/debian/libncbi6.docs
 README
 README.htm
+debian/*.css
+debian/*.gif
 doc/FAQ.txt
 doc/dispatcher.html
 doc/ncbixml.txt
--- a/debian/ncbi-tools-x11.docs
+++ b/debian/ncbi-tools-x11.docs
+debian/*.css
+debian/*.gif
 doc/fire*
 doc/images
 doc/sequin.htm
--- a/debian/ncbi2.css
+++ b/debian/ncbi2.css
+.TEXT {
+	font-size: 90%;
+	font-family: arial,helvetica,sans-serif;
+	}
+
+.TEXTWIDE {
+	font-size: 90%;
+	font-family: arial,helvetica,sans-serif;
+	}
+
+.medium1 {
+	font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	}
+
+.medium2 {
+	font-size: 75%;
+	font-family: verdana;
+	}
+
+.medium3 {
+	font-size: 75%;
+	font-family: courier;
+	}
+	
+.medium4 {
+	font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	font-style: italic;
+	}
+
+.GUTTER1 {
+	font-size: 85%;
+    font-family: arial,helvetica,sans-serif;
+    color:#ffcc66;
+	}
+
+.GUTTER2 {
+	font-size: 75%;
+        font-family: arial,helvetica,sans-serif;
+	color:#ccccff;
+	}
+    
+.GUTTER3 {
+	font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	color:#ffffff;
+	text-decoration:none;
+	}
+
+A	{
+	color:#0033CC;
+	}
+	
+A.BOOK	{
+	color:#085a29;
+	font-weight: bold;
+	}
+
+A.BAR {
+	font-size:85%;
+	color:#ffffff;
+	font-family: arial,helvetica,sans-serif;
+	text-decoration:none;
+	}
+
+A.HELPBAR {
+	color:#000000;
+        font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	text-decoration:none;
+	}
+
+A.GUTTER {
+	color:#ffffff;
+        font-size: 85%;
+	font-family: arial,helvetica,sans-serif;
+        text-decoration:none;
+        }   
+   
+A.GUTTER1 {
+	color:#ffcc66;
+	font-size:85%;
+	font-family: arial,helvetica,sans-serif;
+	text-decoration:none;
+	}
+
+A.GUTTER2 {
+	font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	color:#ccccff;
+	text-decoration:none;
+	}
+	
+A.GUTTER3 {
+	font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	color:#ffffff;
+	text-decoration:none;
+	}
+
+A.BUTTON {
+	font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	color:#000000;
+	text-decoration:none;
+	}
+
+H1, .H1 {
+	font-size: 125%;
+	font-weight: bold;
+	font-family: arial,helvetica,sans-serif;
+	}
+
+H2, .H2 {
+	font-size: 125%;
+	font-weight: bold;
+	font-family: arial,helvetica,sans-serif;
+	}
+
+H3, .H3 {
+	font-size: 100%;
+	font-weight: bold;
+	font-family: arial,helvetica,sans-serif;
+	}
+
+H4, .H4 {
+	font-size: 100%;
+	font-weight: bold;
+	font-family: arial,helvetica,sans-serif;
+	}
+
+H5, .H5 {
+	font-size: 85%;
+	font-weight: bold;
+	font-style: italic;
+	font-family: arial,helvetica,sans-serif;
+	}
+	
+.pmlinka {
+	font-family: arial,helvetica,sans-serif;
+	font-size:85%;
+	font-weight:bold;
+	color: #336699;
+	text-align:center;
+	vertical-align:baseline;                        
+	text-decoration:none;
+	}
+
+.pmlinkna {
+	font-family: arial,helvetica,sans-serif;
+	font-size:85%;
+	color: #336699;
+	text-align:center;
+	vertical-align:baseline;
+	text-decoration:none;
+	}
+
+.taba {
+	background:#FFFFFF;
+ 	text-align:center;
+	vertical-align:baseline;
+	}
+
+.tabna {
+	background:#CCCCCC;
+	text-align:center;
+	vertical-align:baseline;
+	}
+
+.dblinks {        
+	font-size: 75%;
+	font-family: arial,helvetica,sans-serif;
+	color:#336699;
+	text-decoration:none;
+	}
+
+A.popmenu:link { text-decoration: none; font-family: Verdana, Arial, Sans-serif; font-size: 11px; color: Navy; }
+A.popmenu:visited { text-decoration: none; font-family: Verdana, Arial, Sans-serif; font-size: 11px;  color:#6C7F9A; }
+A.popmenu:active { text-decoration: none; font-family: Verdana, Arial, Sans-serif; font-size: 11px;  color:#001A4F; }
+A.popmenu:hover { text-decoration: underline; color:#038000;  font-family: Verdana, Arial, Sans-serif; font-size: 11px; }
+.menutitle { font-family: Verdana, Arial, Sans-serif; font-size: 10px;  font-weight: bold; }
+.fixedsize_skobka { color:#000084; font-size:10px; font-family:Arial,sans-serif; }
+
--- a/debian/patches/debian-changes
+++ b/debian/patches/debian-changes
@@ -209,6 +209,26 @@ Combined patches from git.
   } else if (useTestServ) {
     EntrezSetService ("Entrez2Test");
   } else if (useURL) {
+--- ncbi-tools6-6.1.20170106.orig/demo/findspl.c
+++ ncbi-tools6-6.1.20170106/demo/findspl.c
+@@ -62,6 +62,8 @@
+ #include <accentr.h>
+ #include <sequtil.h>
+ 
+#include <connect/ncbi_gnutls.h>
+
+ #define NUMARGS 3
+ Args myargs[NUMARGS] = {
+         {"Gi number of protein","0","1","99999999",FALSE,'g',ARG_INT,0.0,0,NULL},
+@@ -98,6 +100,8 @@ Int2 Main(void)
+ 	FILE *ofp;
+ 	FILE *ifp = NULL;
+ 
+	SOCK_SetupSSL(NcbiSetupGnuTls);
+
+ 	if ( !GetArgs("findspl", NUMARGS, myargs) ) return 1;
+ 
+ 	gi = myargs[0].intvalue;
 --- ncbi-tools6-6.1.20170106.orig/demo/gbseqget.c
 +++ ncbi-tools6-6.1.20170106/demo/gbseqget.c
 @@ -54,6 +54,8 @@
@@ -269,6 +289,26 @@ Combined patches from git.
   if (! AllObjLoad ()) {
     Message (MSG_FATAL, "AllObjLoad failed");
     return 1;
+--- ncbi-tools6-6.1.20170106.orig/demo/taxblast_main.c
+++ ncbi-tools6-6.1.20170106/demo/taxblast_main.c
+@@ -41,6 +41,8 @@ static char const rcsid[] = "$Id: taxbla
+ #include <objgen.h>
+ #include <taxblast.h>
+ 
+#include <connect/ncbi_gnutls.h>
+
+ 
+ #define NUMARG (sizeof(myargs)/sizeof(myargs[0]))
+ 
+@@ -63,6 +65,8 @@ Int2 Main (void)
+     FILE *outfile;
+     Char ofile[128];
+     
+    SOCK_SetupSSL(NcbiSetupGnuTls);
+
+     if (!GetArgs("txblast", NUMARG, myargs)) {
+         return 1;
+     }
 --- ncbi-tools6-6.1.20170106.orig/demo/tbl2asn.c
 +++ ncbi-tools6-6.1.20170106/demo/tbl2asn.c
 @@ -8911,10 +8911,12 @@ Int2 Main (void)
@@ -313,8 +353,81 @@ Combined patches from git.
         exit(-1);
     }
   }
+--- ncbi-tools6-6.1.20170106.orig/doc/dispatcher.html
+++ ncbi-tools6-6.1.20170106/doc/dispatcher.html
+@@ -9,15 +9,15 @@
+ -->
+   <META NAME="keywords" CONTENT="dispatcher toolkit">
+   <META NAME="description" CONTENT="NCBI dispatcher">
+-  <link rel="stylesheet" href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi2.css">
+  <link rel="stylesheet" href="ncbi2.css">
+ </head>
+ 
+ 
+-<body bgcolor="#FFFFFF" background="http://www.ncbi.nlm.nih.gov/corehtml/bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
+<body bgcolor="#FFFFFF" background="bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
+ <!--  the header   --> 
+ <table border="0" width="600" cellspacing="0" cellpadding="0">
+   <tr> 
+-    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
+    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="left.gif" width="130" height="45" border="0"></a></td>
+     <td width="360" class="head1" valign="BOTTOM"> <span class="H1">Network Configuration</span></td>
+     <td width="100" valign="BOTTOM"></td>
+   </tr>
+@@ -37,7 +37,7 @@
+ <table border="0" width="600" cellspacing="0" cellpadding="0">
+   <tr valign="TOP"> <!--  left column   --> 
+     <td width="125"> 
+-   <img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="125" height="1" border="0">
+   <img src="spacer10.gif" width="125" height="1" border="0">
+    <p>
+    <a href="#Switch" class="GUTTER">The Switch</a>
+    <p>
+@@ -52,7 +52,7 @@
+    <a href="#Addendum" class="GUTTER">Additional Info</a>
+    </td>
+     <!-- extra column to force things over the gif border --> 
+-    <td width="15"><img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="15" height="1" border="0"> </td>
+    <td width="15"><img src="spacer10.gif" width="15" height="1" border="0"> </td>
+     <!-- right content column  --> 
+     <td width="460"> 
+       <p>&nbsp;</p>
 --- ncbi-tools6-6.1.20170106.orig/doc/firewall.html
 +++ ncbi-tools6-6.1.20170106/doc/firewall.html
+@@ -9,15 +9,15 @@
+  <META NAME="keywords" CONTENT="insert your keywords for the search engine">
+  <META NAME="description" CONTENT="insert the description to be displayed by the search engine.  Also searched by the search engine.">
+ -->
+-  <link rel="stylesheet" href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi2.css">
+  <link rel="stylesheet" href="ncbi2.css">
+ </head>
+ 
+ 
+-<body bgcolor="#FFFFFF" background="http://www.ncbi.nlm.nih.gov/corehtml/bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
+<body bgcolor="#FFFFFF" background="bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
+ <!--  the header   --> 
+ <table border="0" width="600" cellspacing="0" cellpadding="0">
+   <tr> 
+-    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
+    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="left.gif" width="130" height="45" border="0"></a></td>
+     <td width="360" class="head1" valign="BOTTOM"> <span class="H1">Network Configuration</span></td>
+     <td width="100" valign="BOTTOM"></td>
+   </tr>
+@@ -37,12 +37,12 @@
+ <table border="0" width="600" cellspacing="0" cellpadding="0">
+   <tr valign="TOP"> <!--  left column   --> 
+     <td width="125"> 
+-<img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="125" height="1" border="0">
+<img src="spacer10.gif" width="125" height="1" border="0">
+ 
+ 
+    </td>
+     <!-- extra column to force things over the gif border --> 
+-    <td width="15"><img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="15" height="1" border="0"> </td>
+    <td width="15"><img src="spacer10.gif" width="15" height="1" border="0"> </td>
+     <!-- right content column  --> 
+     <td width="460"> 
+       <p>&nbsp;</p>
 @@ -133,7 +133,7 @@ in case the public access will eventuall
 
 <p>
@@ -492,6 +605,16 @@ Combined patches from git.
 #
 #	$Id: makedemo.unx,v 6.96 2016/08/31 19:05:26 ucko Exp $
 #
+@@ -228,7 +228,8 @@ cdscan : cdscan.c
+ # findspl
+ 
+ findspl : findspl.c
+-	$(CC) -o findspl $(LDFLAGS) findspl.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
+	$(CC) -o findspl $(LDFLAGS) findspl.c $(ENTREZLIBS) $(LIB2) $(LIB1) \
+	    $(LIBTLS) $(OTHERLIBS)
+ 
+ # errhdr
+ 
 --- ncbi-tools6-6.1.20170106.orig/make/makenet.unx
 +++ ncbi-tools6-6.1.20170106/make/makenet.unx
 @@ -1,4 +1,4 @@
@@ -830,23 +953,3 @@ Combined patches from git.
   Nlm_RegisterWindows ();
   Nlm_RegisterTexts ();
   Nlm_RegisterSlates ();
--- ncbi-tools6-6.1.20170106.orig/demo/taxblast_main.c
-+++ ncbi-tools6-6.1.20170106/demo/taxblast_main.c
-@@ -41,6 +41,8 @@ static char const rcsid[] = "$Id: taxbla
- #include <objgen.h>
- #include <taxblast.h>
- 
-+#include <connect/ncbi_gnutls.h>
-+
- 
- #define NUMARG (sizeof(myargs)/sizeof(myargs[0]))
- 
-@@ -63,6 +65,8 @@ Int2 Main (void)
-     FILE *outfile;
-     Char ofile[128];
-     
-+    SOCK_SetupSSL(NcbiSetupGnuTls);
-+
-     if (!GetArgs("txblast", NUMARG, myargs)) {
-         return 1;
-     }
--- a/debian/source/include-binaries
+++ b/debian/source/include-binaries
+debian/bkgd.gif
+debian/left.gif
+debian/spacer10.gif
 debian/tests/test-data/nc0225.aso.gz
 debian/tests/test-data/dsRNA_viruses.ags.gz
 debian/tests/test-data/dsRNA_viruses.gene_info.gz

--- a/debian/spacer10.gif
+++ b/debian/spacer10.gif
--- a/demo/findspl.c
+++ b/demo/findspl.c
@@ -62,6 +62,8 @@
 #include <accentr.h>
 #include <sequtil.h>

+#include <connect/ncbi_gnutls.h>
+
 #define NUMARGS 3
 Args myargs[NUMARGS] = {
        {"Gi number of protein","0","1","99999999",FALSE,'g',ARG_INT,0.0,0,NULL},
@@ -98,6 +100,8 @@ Int2 Main(void)
 	FILE *ofp;
 	FILE *ifp = NULL;

+	SOCK_SetupSSL(NcbiSetupGnuTls);
+
 	if ( !GetArgs("findspl", NUMARGS, myargs) ) return 1;

 	gi = myargs[0].intvalue;

--- a/doc/dispatcher.html
+++ b/doc/dispatcher.html
@@ -9,15 +9,15 @@
 -->
  <META NAME="keywords" CONTENT="dispatcher toolkit">
  <META NAME="description" CONTENT="NCBI dispatcher">
-  <link rel="stylesheet" href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi2.css">
+  <link rel="stylesheet" href="ncbi2.css">
 </head>


-<body bgcolor="#FFFFFF" background="http://www.ncbi.nlm.nih.gov/corehtml/bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
+<body bgcolor="#FFFFFF" background="bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
 <!--  the header   --> 
 <table border="0" width="600" cellspacing="0" cellpadding="0">
  <tr> 
-    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
+    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="left.gif" width="130" height="45" border="0"></a></td>
    <td width="360" class="head1" valign="BOTTOM"> <span class="H1">Network Configuration</span></td>
    <td width="100" valign="BOTTOM"></td>
  </tr>
@@ -37,7 +37,7 @@
 <table border="0" width="600" cellspacing="0" cellpadding="0">
  <tr valign="TOP"> <!--  left column   --> 
    <td width="125"> 
-   <img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="125" height="1" border="0">
+   <img src="spacer10.gif" width="125" height="1" border="0">
   <p>
   <a href="#Switch" class="GUTTER">The Switch</a>
   <p>
@@ -52,7 +52,7 @@
   <a href="#Addendum" class="GUTTER">Additional Info</a>
   </td>
    <!-- extra column to force things over the gif border --> 
-    <td width="15"><img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="15" height="1" border="0"> </td>
+    <td width="15"><img src="spacer10.gif" width="15" height="1" border="0"> </td>
    <!-- right content column  --> 
    <td width="460"> 
      <p>&nbsp;</p>

--- a/doc/firewall.html
+++ b/doc/firewall.html
@@ -9,15 +9,15 @@
 <META NAME="keywords" CONTENT="insert your keywords for the search engine">
 <META NAME="description" CONTENT="insert the description to be displayed by the search engine.  Also searched by the search engine.">
 -->
-  <link rel="stylesheet" href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi2.css">
+  <link rel="stylesheet" href="ncbi2.css">
 </head>


-<body bgcolor="#FFFFFF" background="http://www.ncbi.nlm.nih.gov/corehtml/bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
+<body bgcolor="#FFFFFF" background="bkgd.gif" text="#000000" link="#CC6600" vlink="#CC6600">
 <!--  the header   --> 
 <table border="0" width="600" cellspacing="0" cellpadding="0">
  <tr> 
-    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
+    <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="left.gif" width="130" height="45" border="0"></a></td>
    <td width="360" class="head1" valign="BOTTOM"> <span class="H1">Network Configuration</span></td>
    <td width="100" valign="BOTTOM"></td>
  </tr>
@@ -37,12 +37,12 @@
 <table border="0" width="600" cellspacing="0" cellpadding="0">
  <tr valign="TOP"> <!--  left column   --> 
    <td width="125"> 
-<img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="125" height="1" border="0">
+<img src="spacer10.gif" width="125" height="1" border="0">


   </td>
    <!-- extra column to force things over the gif border --> 
-    <td width="15"><img src="http://www.ncbi.nlm.nih.gov/corehtml/spacer10.GIF" width="15" height="1" border="0"> </td>
+    <td width="15"><img src="spacer10.gif" width="15" height="1" border="0"> </td>
    <!-- right content column  --> 
    <td width="460"> 
      <p>&nbsp;</p>

--- a/make/makedemo.unx
+++ b/make/makedemo.unx
@@ -228,7 +228,8 @@ cdscan : cdscan.c
 # findspl

 findspl : findspl.c
-	$(CC) -o findspl $(LDFLAGS) findspl.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
+	$(CC) -o findspl $(LDFLAGS) findspl.c $(ENTREZLIBS) $(LIB2) $(LIB1) \
+	    $(LIBTLS) $(OTHERLIBS)

 # errhdr