############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CNEr.buildbin-libdir && mkdir CNEr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNEr_1.30.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNEr.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNEr.buildbin-libdir CNEr_1.30.0.tar.gz' >>>>>>> * installing *source* package ‘CNEr’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c R_init_CNEr.c -o R_init_CNEr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c utils.c -o utils.o utils.c:50:7: warning: unused variable '_binNextShift' [-Wunused-variable] int _binNextShift = binNextShift(); ^ utils.c:49:7: warning: unused variable '_binFirstShift' [-Wunused-variable] int _binFirstShift = binFirstShift(); ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ceScan.c -o ceScan.o ceScan.c:615:8: warning: unused variable 'rest' [-Wunused-variable] char rest, path[PATH_LEN]; ^ ceScan.c:613:10: warning: unused variable 'n' [-Wunused-variable] int i, n; ^ ceScan.c:674:17: warning: unused variable 'CNE' [-Wunused-variable] struct slCNE *CNE, *nextCNE, *el_CNE; ^ ceScan.c:673:23: warning: unused variable 'thresholds' [-Wunused-variable] struct slThreshold *thresholds, *nextThreshold, *el_threshold; ^ ceScan.c:868:28: warning: unused variable 'i' [-Wunused-variable] int nrCNE[nrThresholds], i; ^ 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:898:7: warning: unused variable 'nrThresholds' [-Wunused-variable] int nrThresholds = GET_LENGTH(winSize); ^ 8 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/axt.c -o ucsc/axt.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/chain.c -o ucsc/chain.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/hash.c -o ucsc/hash.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/https.c -o ucsc/https.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/intExp.c -o ucsc/intExp.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/kxTok.c -o ucsc/kxTok.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/options.c -o ucsc/options.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/sqlList.c -o ucsc/sqlList.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/os.c -o ucsc/os.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I/usr/local/include -g -fPIC -Wall -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o clang -mmacosx-version-min=10.13 -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 /Users/biocbuild/bbs-3.14-bioc/meat/CNEr.buildbin-libdir/00LOCK-CNEr/00new/CNEr/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CNEr) >>>>>>> >>>>>>> FIXING LINKS FOR CNEr.buildbin-libdir/CNEr/libs/CNEr.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "CNEr.buildbin-libdir/CNEr/libs/CNEr.so"