Add LICENSE info and R CMD check fix
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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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/* 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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/* 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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/* 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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/* 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" |