CNEr 1.10.2
Ge Tan
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/CNEr | | Last Changed Rev: 127452 / Revision: 128728 | | Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | [ OK ] | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNEr
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘CNEr’ ...
** 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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c S4Vectors_stubs.c -o S4Vectors_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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c R_init_CNEr.c -o R_init_CNEr.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c utils.c -o utils.o
utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable]
int _binFirstShift = binFirstShift();
^
utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable]
int _binNextShift = binNextShift();
^
2 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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c io.c -o io.o
io.c:94:26: warning: unused variable 'curAxt' [-Wunused-variable]
struct axt *axt=NULL, *curAxt;
^
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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ceScan.c -o ceScan.o
ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable]
int i, n;
^
ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable]
char rest, path[PATH_LEN];
^
ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable]
struct slThreshold *thresholds, *nextThreshold, *el_threshold;
^
ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE, *nextCNE, *el_CNE;
^
ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:865:17: warning: unused variable 'CNE' [-Wunused-variable]
struct slCNE *CNE;
^
ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable]
int nrCNE[nrThresholds], i;
^
ceScan.c:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable]
int nrThresholds = GET_LENGTH(winSize);
^
8 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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/axt.c -o ucsc/axt.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/base64.c -o ucsc/base64.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/binRange.c -o ucsc/binRange.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/bits.c -o ucsc/bits.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/chain.c -o ucsc/chain.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:472:16: warning: unused function 'cirTreeOverlaps' [-Wunused-function]
INLINE boolean cirTreeOverlaps(int qChrom, int qStart, int qEnd,
^
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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:1982:18: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*in == '"'))
˜˜˜˜^˜˜˜˜˜
ucsc/common.c:1982:18: note: remove extraneous parentheses around the comparison to silence this warning
if ((*in == '"'))
˜ ^ ˜
ucsc/common.c:1982:18: note: use '=' to turn this equality comparison into an assignment
if ((*in == '"'))
^˜
=
ucsc/common.c:2842:14: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2843:14: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2844:14: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2845:14: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2846:1: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2847:1: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2848:1: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2849:1: 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:2840:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2976:14: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2977:14: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2978:14: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2979:14: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2980:1: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2981:1: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2982:1: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2983:1: 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:2974:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
17 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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dlist.c -o ucsc/dlist.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/dystring.c -o ucsc/dystring.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/hash.c -o ucsc/hash.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/intExp.c -o ucsc/intExp.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/kxTok.c -o ucsc/kxTok.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/localmem.c -o ucsc/localmem.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/obscure.c -o ucsc/obscure.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/options.c -o ucsc/options.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/sqlList.c -o ucsc/sqlList.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/verbose.c -o ucsc/verbose.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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -g -fPIC -Wall -mtune=core2 -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CNEr.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/CNEr/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNEr)