############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CNEr ### ############################################################################## ############################################################################## * checking for file ‘CNEr/DESCRIPTION’ ... OK * preparing ‘CNEr’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘CNEr’ ... ** this is package ‘CNEr’ version ‘1.45.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_CNEr.c -o R_init_CNEr.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -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 -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -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 -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -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:865:17: warning: unused variable 'CNE' [-Wunused-variable] struct slCNE *CNE; ^ ceScan.c:868:7: warning: unused variable 'nrCNE' [-Wunused-variable] int nrCNE[nrThresholds], i; ^ 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 -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/axt.c -o ucsc/axt.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/chain.c -o ucsc/chain.o ucsc/chain.c:399:5: warning: variable 'usedCount' set but not used [-Wunused-but-set-variable] int usedCount = 0, count = 0; ^ ucsc/chain.c:399:20: warning: variable 'count' set but not used [-Wunused-but-set-variable] int usedCount = 0, count = 0; ^ 2 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o ucsc/cirTree.c:475:16: warning: unused function 'cirTreeOverlaps' [-Wunused-function] INLINE boolean cirTreeOverlaps(int qChrom, int qStart, int qEnd, ^ 1 warning generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -g -fPIC -falign-functions=64 -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o ucsc/common.c:360:14: error: too many arguments to function call, expected 0, have 1 free(el); ~~~~ ^~ 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 == '"')) ^~ = 1 warning and 1 error generated. make: *** [ucsc/common.o] Error 1 ERROR: compilation failed for package ‘CNEr’ * removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpWGYkbD/Rinst12a947902db72/CNEr’ ----------------------------------- ERROR: package installation failed