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version 1.33.1

Add LICENSE info and R CMD check fix

Ge Tan authored on 23/10/2022 22:33:22
Showing 16 changed files

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@@ -1,6 +1,6 @@
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 Package: CNEr 
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-Version: 1.33.0
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-Date: 2021-11-20
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+Version: 1.33.1
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+Date: 2022-10-23
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 Title: CNE Detection and Visualization
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 Description: Large-scale identification and advanced visualization 
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              of sets of conserved noncoding elements.
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 CONTENTS AND COPYRIGHT
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-The source code under src/ucsc comes from Jim Kent's source utilities.
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+The source code under "src/ucsc" comes from Jim Kent's source utilities.
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 Any usage of this code should follow the license restriction.
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+Note that the "src/lib", "src/inc" and "src/utils" refer to directories within
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+the original Kent source tree. In CNEr, the files are all under
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+"src/ucsc".
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 The following lines are taken from README of Kent's utilities.
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@@ -11,7 +14,4 @@ and web display programs as well as some of Jim Kent's own tools.
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 All files are copyrighted, but license is hereby granted for personal,
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 academic, and non-profit use.  A license is also granted for the contents
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 of the src/lib, src/inc and src/utils and python directories for commercial
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-users.  Commercial users should contact kent@soe.ucsc.edu for access to other
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-modules.  Commercial users interested in the UCSC Genome Browser in particular
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-please see
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-    http://genome.ucsc.edu/license/.
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+users.
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 }
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 \examples{
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-  \donttest{
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+  \dontrun{
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     library(GO.db)
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     go <- list(c("GO:0005215", "GO:0006810", "GO:0016020"), "GO:0016579")
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     addAncestorGO(go)
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 }
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 \examples{
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-  \donttest{
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+  \dontrun{
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     orgKEGGIds2EntrezIDs(organism="Homo sapiens")
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   }
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 }
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 /* rtracklayer took out these little utilities from cheapcgi.c */
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+/* Routines for getting variables passed in from web page
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+ * forms via CGI.
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+ *
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+ * This file is copyright 2002 Jim Kent, but license is hereby
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+ * granted for all use - public, private or commercial. */
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+
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 #include "common.h"
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 void cgiDecode(char *in, char *out, int inLength)
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 /* rtracklayer took this utility out of portimpl.c */
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+/* Implementation file for some portability stuff mostly aimed
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+ * at making the same code run under different web servers.
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+ *
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+ * This file is copyright 2002 Jim Kent, but license is hereby
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+ * granted for all use - public, private or commercial. */
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+
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 #include "common.h"
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 #include "portable.h"
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+/* Copyright (C) 2011 The Regents of the University of California 
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+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
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+
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 #include "common.h"
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 #include "base64.h"
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 /* chain - pairwise alignments that can include gaps in both
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  * sequences at once.  This is similar in many ways to psl,
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  * but more suitable to cross species genomic comparisons. */
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+
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+/* Copyright (C) 2011 The Regents of the University of California 
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+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
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 #include "common.h"
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 #include "linefile.h"
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 #include "hash.h"
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  * as the most significant part of a two-part key, and the base position as the least 
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  * significant part of the key. */
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+/* Copyright (C) 2014 The Regents of the University of California 
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+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
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+
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 #include "common.h"
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 #include "localmem.h"
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 #include "sig.h"
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 bits64 byteSwap64(bits64 a)
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 /* Return byte-swapped version of a */
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 {
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-union {bits64 whole; UBYTE bytes[4];} u,v;
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+union {bits64 whole; UBYTE bytes[8];} u,v;
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 u.whole = a;
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 v.bytes[0] = u.bytes[7];
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 v.bytes[1] = u.bytes[6];
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 double byteSwapDouble(double a)
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 /* Return byte-swapped version of a */
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 {
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-union {double whole; UBYTE bytes[4];} u,v;
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+union {double whole; UBYTE bytes[8];} u,v;
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 u.whole = a;
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 v.bytes[0] = u.bytes[7];
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 v.bytes[1] = u.bytes[6];
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 /* Connect via https. */
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+/* Copyright (C) 2012 The Regents of the University of California 
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+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
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+
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 #ifdef USE_SSL
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 #include "openssl/ssl.h"
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 /* internet - some stuff to make it easier to use
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  * internet sockets and the like. */
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+
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+/* Copyright (C) 2011 The Regents of the University of California 
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+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
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 #include "common.h"
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 #include "internet.h"
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 /* Added by rtracklayer to condition on the platform */
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+/* License: Artistic-2.0 */
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 #ifdef WIN32
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 #include "oswin9x.c"
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 /* pipeline.c - create a process pipeline that can be used for reading or
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  * writing  */
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+
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+/* Copyright (C) 2013 The Regents of the University of California 
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+ * See README in this or parent directory for licensing information. */
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+
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 #include "pipeline.h"
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 #include "common.h"
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 #include "sqlNum.h"
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+/* Copyright (C) 2014 The Regents of the University of California 
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+ * See README in this or parent directory for licensing information. */
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+
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 /* udc - url data cache - a caching system that keeps blocks of data fetched from URLs in
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  * sparse local files for quick use the next time the data is needed. 
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  *
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 /* verbose.c - write out status messages according to the
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  * current verbosity level.  These messages go to stderr. */
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+/* Copyright (C) 2011 The Regents of the University of California 
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+ * See README in this or parent directory for licensing information. */
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+
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 #include "common.h"
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 #include "portable.h"
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 #include "verbose.h"