rtracklayer 1.24.2
Michael Lawrence
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/rtracklayer | | Last Changed Rev: 90983 / Revision: 95116 | | Last Changed Date: 2014-06-04 05:18:23 -0700 (Wed, 04 Jun 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | [ OK ] | OK | WARNINGS | OK |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
* installing *source* package ‘rtracklayer’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c bigWig.c -o bigWig.o
bigWig.c:202:8: warning: unused variable 'numericList' [-Wunused-variable]
SEXP numericList, numericListEls;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c chain_io.c -o chain_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c twoBit.c -o twoBit.o
twoBit.c:109:37: warning: passing 'Rbyte *' (aka 'unsigned char *') to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
RAW(r_seq), total_width,
^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include/XVector_interface.h:84:8: note: passing argument to parameter 'dest' here
char *dest,
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c handlers.c -o handlers.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c utils.c -o utils.o
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
SEXP ans;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
ucsc/bwgCreate.c:18:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: bwgCreate.c,v 1.27 2010/06/10 20:13:29 braney Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c:23:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: bwgQuery.c,v 1.24 2010/06/03 18:08:37 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1910:17: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((*in == '"'))
˜˜˜˜^˜˜˜˜˜
ucsc/common.c:1910:17: note: remove extraneous parentheses around the comparison to silence this warning
if((*in == '"'))
˜ ^ ˜
ucsc/common.c:1910:17: note: use '=' to turn this equality comparison into an assignment
if((*in == '"'))
^˜
=
ucsc/common.c:2765:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2766:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2767:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2768:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2769:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2770:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2771:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2772:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2899:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2900:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2901:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2902:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2903:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2904:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2905:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2906:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:102:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:13:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: common.c,v 1.151 2010/06/02 19:06:41 tdreszer Exp $";
^
18 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
ucsc/dnaseq.c:12:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: dnaseq.c,v 1.20 2008/10/30 09:27:59 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:18:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: dnautil.c,v 1.51 2008/10/24 18:20:17 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/hash.c -o ucsc/hash.o
ucsc/hash.c:12:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: hash.c,v 1.51 2009/11/10 22:46:19 angie Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c:14:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: localmem.c,v 1.13 2009/12/03 20:04:29 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
ucsc/sqlNum.c:10:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: sqlNum.c,v 1.17 2010/05/17 18:01:41 hiram Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o
ucsc/dystring.c:9:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: dystring.c,v 1.25 2009/11/13 19:01:56 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
ucsc/hmmstats.c:10:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: hmmstats.c,v 1.5 2009/02/03 20:50:29 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c:14:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: obscure.c,v 1.53 2010/01/27 21:04:04 galt Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
ucsc/rangeTree.c:17:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: rangeTree.c,v 1.24 2009/02/01 01:34:21 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o
ucsc/rbTree.c:12:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: rbTree.c,v 1.12 2008/10/16 02:39:51 kent Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c:16:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: memalloc.c,v 1.31 2007/04/24 18:35:43 hiram Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o
ucsc/dlist.c:8:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: dlist.c,v 1.11 2005/07/04 18:44:09 markd Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c:138:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (rd < 0)
˜˜ ^ ˜
ucsc/udc.c:384:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (retInfo->size < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/udc.c:44:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: udc.c,v 1.37 2010/03/19 19:16:37 angie Exp $";
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/net.c -o ucsc/net.o
ucsc/net.c:2350:37: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (netReadAll(sd, buf, length) < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/net.c:2379:35: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (netReadAll(sd, s, length) < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/net.c:2412:35: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (netReadAll(sd, s, length) < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/net.c:26:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: net.c,v 1.80 2010/04/14 07:42:06 galt Exp $";
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/bits.c -o ucsc/bits.o
ucsc/bits.c:9:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: bits.c,v 1.20 2008/03/25 16:32:31 angie Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o
ucsc/twoBit.c:13:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: twoBit.c,v 1.28 2009/09/23 18:42:29 angie Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/internet.c -o ucsc/internet.o
ucsc/internet.c:8:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: internet.c,v 1.11 2010/03/11 17:54:35 angie Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/https.c -o ucsc/https.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/base64.c -o ucsc/base64.o
ucsc/base64.c:4:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: base64.c,v 1.6 2008/09/17 18:00:47 galt Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o
ucsc/verbose.c:8:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: verbose.c,v 1.7 2010/04/01 17:31:10 markd Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/os.c -o ucsc/os.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
ucsc/wildcmp.c:8:19: warning: unused variable 'rcsid' [-Wunused-const-variable]
static char const rcsid[] = "$Id: wildcmp.c,v 1.7 2009/11/20 19:11:16 angie Exp $";
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rtracklayer.so IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)