@@ -1,6 +1,6 @@

 Package: CNEr 

-Version: 1.33.0

-Date: 2021-11-20

+Version: 1.33.1

+Date: 2022-10-23

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

@@ -1,7 +1,10 @@

 CONTENTS AND COPYRIGHT

-The source code under src/ucsc comes from Jim Kent's source utilities.

+The source code under "src/ucsc" comes from Jim Kent's source utilities.

 Any usage of this code should follow the license restriction.

+Note that the "src/lib", "src/inc" and "src/utils" refer to directories within

+the original Kent source tree. In CNEr, the files are all under

+"src/ucsc".

 The following lines are taken from README of Kent's utilities.

@@ -11,7 +14,4 @@ and web display programs as well as some of Jim Kent's own tools.

 All files are copyrighted, but license is hereby granted for personal,

 academic, and non-profit use.  A license is also granted for the contents

 of the src/lib, src/inc and src/utils and python directories for commercial

-users.  Commercial users should contact kent@soe.ucsc.edu for access to other

-modules.  Commercial users interested in the UCSC Genome Browser in particular

-please see

-    http://genome.ucsc.edu/license/.

+users.

@@ -31,7 +31,7 @@

 }

 \examples{

-  \donttest{

+  \dontrun{

     library(GO.db)

     go <- list(c("GO:0005215", "GO:0006810", "GO:0016020"), "GO:0016579")

     addAncestorGO(go)

@@ -25,7 +25,7 @@

 }

 \examples{

-  \donttest{

+  \dontrun{

     orgKEGGIds2EntrezIDs(organism="Homo sapiens")

   }

 }

@@ -1,5 +1,11 @@

 /* rtracklayer took out these little utilities from cheapcgi.c */

+/* Routines for getting variables passed in from web page

+ * forms via CGI.

+ *

+ * This file is copyright 2002 Jim Kent, but license is hereby

+ * granted for all use - public, private or commercial. */

+

 #include "common.h"

 void cgiDecode(char *in, char *out, int inLength)

@@ -1,5 +1,11 @@

 /* rtracklayer took this utility out of portimpl.c */

+/* Implementation file for some portability stuff mostly aimed

+ * at making the same code run under different web servers.

+ *

+ * This file is copyright 2002 Jim Kent, but license is hereby

+ * granted for all use - public, private or commercial. */

+

 #include "common.h"

 #include "portable.h"

@@ -1,3 +1,6 @@

+/* Copyright (C) 2011 The Regents of the University of California 

+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

+

 #include "common.h"

 #include "base64.h"

@@ -1,6 +1,9 @@

 /* chain - pairwise alignments that can include gaps in both

  * sequences at once.  This is similar in many ways to psl,

  * but more suitable to cross species genomic comparisons. */

+

+/* Copyright (C) 2011 The Regents of the University of California 

+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

 #include "common.h"

 #include "linefile.h"

 #include "hash.h"

@@ -8,6 +8,9 @@

  * as the most significant part of a two-part key, and the base position as the least 

  * significant part of the key. */

+/* Copyright (C) 2014 The Regents of the University of California 

+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

+

 #include "common.h"

 #include "localmem.h"

 #include "sig.h"

@@ -2837,7 +2837,7 @@ return ret;

 bits64 byteSwap64(bits64 a)

 /* Return byte-swapped version of a */

 {

-union {bits64 whole; UBYTE bytes[4];} u,v;

+union {bits64 whole; UBYTE bytes[8];} u,v;

 u.whole = a;

 v.bytes[0] = u.bytes[7];

 v.bytes[1] = u.bytes[6];

@@ -2971,7 +2971,7 @@ return val;

 double byteSwapDouble(double a)

 /* Return byte-swapped version of a */

 {

-union {double whole; UBYTE bytes[4];} u,v;

+union {double whole; UBYTE bytes[8];} u,v;

 u.whole = a;

 v.bytes[0] = u.bytes[7];

 v.bytes[1] = u.bytes[6];

@@ -1,5 +1,8 @@

 /* Connect via https. */

+/* Copyright (C) 2012 The Regents of the University of California 

+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

+

 #ifdef USE_SSL

 #include "openssl/ssl.h"

@@ -1,5 +1,8 @@

 /* internet - some stuff to make it easier to use

  * internet sockets and the like. */

+

+/* Copyright (C) 2011 The Regents of the University of California 

+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

 #include "common.h"

 #include "internet.h"

@@ -1,4 +1,5 @@

 /* Added by rtracklayer to condition on the platform */

+/* License: Artistic-2.0 */

 #ifdef WIN32

 #include "oswin9x.c"

@@ -2,6 +2,10 @@

 /* pipeline.c - create a process pipeline that can be used for reading or

  * writing  */

+

+/* Copyright (C) 2013 The Regents of the University of California 

+ * See README in this or parent directory for licensing information. */

+

 #include "pipeline.h"

 #include "common.h"

 #include "sqlNum.h"

@@ -1,3 +1,6 @@

+/* Copyright (C) 2014 The Regents of the University of California 

+ * See README in this or parent directory for licensing information. */

+

 /* udc - url data cache - a caching system that keeps blocks of data fetched from URLs in

  * sparse local files for quick use the next time the data is needed. 

  *

@@ -1,6 +1,9 @@

 /* verbose.c - write out status messages according to the

  * current verbosity level.  These messages go to stderr. */

+/* Copyright (C) 2011 The Regents of the University of California 

+ * See README in this or parent directory for licensing information. */

+

 #include "common.h"

 #include "portable.h"

 #include "verbose.h"