############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c R_init_CNEr.c -o R_init_CNEr.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o utils.c: In function ‘bin_ranges_from_coord_range_standard’: utils.c:50:7: warning: unused variable ‘_binNextShift’ [-Wunused-variable] 50 | int _binNextShift = binNextShift(); | ^~~~~~~~~~~~~ utils.c:49:7: warning: unused variable ‘_binFirstShift’ [-Wunused-variable] 49 | int _binFirstShift = binFirstShift(); | ^~~~~~~~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c io.c -o io.o io.c: In function ‘myReadAxt’: io.c:94:26: warning: unused variable ‘curAxt’ [-Wunused-variable] 94 | struct axt *axt=NULL, *curAxt; | ^~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ceScan.c -o ceScan.o ceScan.c: In function ‘ceScan’: ceScan.c:615:8: warning: unused variable ‘rest’ [-Wunused-variable] 615 | char rest, path[PATH_LEN]; | ^~~~ ceScan.c:613:10: warning: unused variable ‘n’ [-Wunused-variable] 613 | int i, n; | ^ ceScan.c: In function ‘freeSlThreshold’: ceScan.c:674:17: warning: unused variable ‘CNE’ [-Wunused-variable] 674 | struct slCNE *CNE, *nextCNE, *el_CNE; | ^~~ ceScan.c:673:23: warning: unused variable ‘thresholds’ [-Wunused-variable] 673 | struct slThreshold *thresholds, *nextThreshold, *el_threshold; | ^~~~~~~~~~ ceScan.c: In function ‘myCeScan’: ceScan.c:868:28: warning: unused variable ‘i’ [-Wunused-variable] 868 | int nrCNE[nrThresholds], i; | ^ ceScan.c:868:7: warning: unused variable ‘nrCNE’ [-Wunused-variable] 868 | int nrCNE[nrThresholds], i; | ^~~~~ ceScan.c:865:17: warning: unused variable ‘CNE’ [-Wunused-variable] 865 | struct slCNE *CNE; | ^~~ ceScan.c: In function ‘myCeScanFile’: ceScan.c:898:7: warning: unused variable ‘nrThresholds’ [-Wunused-variable] 898 | int nrThresholds = GET_LENGTH(winSize); | ^~~~~~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/axt.c -o ucsc/axt.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/base64.c -o ucsc/base64.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/binRange.c -o ucsc/binRange.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/bits.c -o ucsc/bits.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/chain.c -o ucsc/chain.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include -g -fpic -g -O2 -Wall -Werror=format-security -c ucsc/common.c -o ucsc/common.o ucsc/common.c: In function ‘slUniqify’: ucsc/common.c:360:9: error: too many arguments to function ‘free’ 360 | free(el); | ^~~~ make: *** [/home/biocbuild/bbs-3.22-bioc/R/etc/Makeconf:202: ucsc/common.o] Error 1 ERROR: compilation failed for package ‘CNEr’ * removing ‘/tmp/RtmpCi1Db6/Rinstbcc9b51c4dcbc/CNEr’ ----------------------------------- ERROR: package installation failed