############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rtracklayer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘rtracklayer’ ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c readGFF.c -o readGFF.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bbiHelper.c -o bbiHelper.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigBedHelper.c -o bigBedHelper.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigBed.c -o bigBed.o bigBed.c: In function ‘BBDFile_write’: bigBed.c:338:10: warning: variable ‘extraIndexListEndOffset’ set but not used [-Wunused-but-set-variable] 338 | bits64 extraIndexListEndOffset = 0; | ^~~~~~~~~~~~~~~~~~~~~~~ bigBed.c: In function ‘BBDFile_query’: bigBed.c:226:22: warning: ‘typeId’ may be used uninitialized in this function [-Wmaybe-uninitialized] 226 | switch(typeId[efIndex]) { | ^ bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized] 236 | INTEGER(lengthIndex)[efIndex] = index + 1; | ^~~~~~~~~~~~~~~~~~~~ bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized in this function [-Wmaybe-uninitialized] 218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:209:7: warning: ‘itemRgb’ may be used uninitialized in this function [-Wmaybe-uninitialized] 209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized in this function [-Wmaybe-uninitialized] 204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized in this function [-Wmaybe-uninitialized] 205 | INTEGER(thickStart)[i] = bed->thickStart; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:198:7: warning: ‘score’ may be used uninitialized in this function [-Wmaybe-uninitialized] 198 | INTEGER(score)[i] = bed->score; | ^~~~~~~~~~~~~~ bigBed.c:257:5: warning: ‘name’ may be used uninitialized in this function [-Wmaybe-uninitialized] 257 | SET_VECTOR_ELT(ans, index++, name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c chain_io.c -o chain_io.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c handlers.c -o handlers.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/memgfx.c -o ucsc/memgfx.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/binRange.c -o ucsc/binRange.o ucsc/binRange.c:49:12: warning: ‘binFromRangeExtended’ defined but not used [-Wunused-function] 49 | static int binFromRangeExtended(int start, int end) | ^~~~~~~~~~~~~~~~~~~~ ucsc/binRange.c:28:12: warning: ‘binFromRangeStandard’ defined but not used [-Wunused-function] 28 | static int binFromRangeStandard(int start, int end) | ^~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/htmlColor.c -o ucsc/htmlColor.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/tokenizer.c -o ucsc/tokenizer.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/asParse.c -o ucsc/asParse.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/basicBed.c -o ucsc/basicBed.o In file included from /usr/include/string.h:535, from ucsc/common.h:33, from ucsc/basicBed.c:14: In function ‘strncpy’, inlined from ‘bedParseRgb’ at ucsc/basicBed.c:449:1: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bigBed.c -o ucsc/bigBed.o ucsc/bigBed.c:326:31: warning: ‘bigBedIntervalsMatchingName’ defined but not used [-Wunused-function] 326 | static struct bigBedInterval *bigBedIntervalsMatchingName(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/bigBed.c:311:16: warning: ‘bbWordIsInHash’ defined but not used [-Wunused-function] 311 | static boolean bbWordIsInHash(char *line, int fieldIx, void *target) | ^~~~~~~~~~~~~~ ucsc/bigBed.c:301:16: warning: ‘bbWordMatchesName’ defined but not used [-Wunused-function] 301 | static boolean bbWordMatchesName(char *line, int fieldIx, void *target) | ^~~~~~~~~~~~~~~~~ ucsc/bigBed.c:252:31: warning: ‘bigBedChunksMatchingNames’ defined but not used [-Wunused-function] 252 | static struct fileOffsetSize *bigBedChunksMatchingNames(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/bigBed.c:241:31: warning: ‘bigBedChunksMatchingName’ defined but not used [-Wunused-function] 241 | static struct fileOffsetSize *bigBedChunksMatchingName(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~~ ucsc/bigBed.c:150:28: warning: ‘bigBedCoverageIntervals’ defined but not used [-Wunused-function] 150 | static struct bbiInterval *bigBedCoverageIntervals(struct bbiFile *bbi, | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o ucsc/bwgQuery.c: In function ‘bigWigIntervalQuery’: ucsc/bwgQuery.c:164:25: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable] 164 | char *blockPt, *blockEnd; | ^~~~~~~~ At top level: ucsc/bwgQuery.c:47:12: warning: ‘bigWigBlockDumpIntersectingRange’ defined but not used [-Wunused-function] 47 | static int bigWigBlockDumpIntersectingRange(boolean isSwapped, char *blockPt, char *blockEnd, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o ucsc/cirTree.c:530:13: warning: ‘rEnumerateBlocks’ defined but not used [-Wunused-function] 530 | static void rEnumerateBlocks(struct cirTreeFile *crt, int level, bits64 indexFileOffset, | ^~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o ucsc/common.c:1971:13: warning: ‘dateAdd’ defined but not used [-Wunused-function] 1971 | static void dateAdd(struct tm *tp,int addYears,int addMonths,int addDays) | ^~~~~~~ ucsc/common.c:1901:14: warning: ‘emptyStr’ defined but not used [-Wunused-variable] 1901 | static char *emptyStr = ""; | ^~~~~~~~ ucsc/common.c:1900:14: warning: ‘naStr’ defined but not used [-Wunused-variable] 1900 | static char *naStr = "n/a"; | ^~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o ucsc/dnautil.c:521:12: warning: ‘findHeadPolyTMaybeMask’ defined but not used [-Wunused-function] 521 | static int findHeadPolyTMaybeMask(DNA *dna, int size, boolean doMask, | ^~~~~~~~~~~~~~~~~~~~~~ ucsc/dnautil.c:465:12: warning: ‘findTailPolyAMaybeMask’ defined but not used [-Wunused-function] 465 | static int findTailPolyAMaybeMask(DNA *dna, int size, boolean doMask, | ^~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o ucsc/errAbort.c: In function ‘getThreadVars’: ucsc/errAbort.c:255:5: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 255 | write(STDERR_FILENO, errMsg, strlen(errMsg)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ At top level: ucsc/errAbort.c:218:13: warning: ‘warnAbortHandler’ defined but not used [-Wunused-function] 218 | static void warnAbortHandler(char *format, va_list args) | ^~~~~~~~~~~~~~~~ ucsc/errAbort.c:210:13: warning: ‘debugAbort’ defined but not used [-Wunused-function] 210 | static void debugAbort() | ^~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o ucsc/obscure.c:14:12: warning: ‘_dotForUserMod’ defined but not used [-Wunused-variable] 14 | static int _dotForUserMod = 100; /* How often does dotForUser() output a dot. */ | ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o ucsc/rangeTree.c:36:14: warning: ‘sumInt’ defined but not used [-Wunused-function] 36 | static void *sumInt(void *a, void *b) | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o ucsc/rbTree.c:680:13: warning: ‘addRefWithContext’ defined but not used [-Wunused-function] 680 | static void addRefWithContext(void *item, void *context) | ^~~~~~~~~~~~~~~~~ ucsc/rbTree.c:674:13: warning: ‘addRef’ defined but not used [-Wunused-function] 674 | static void addRef(void *item) | ^~~~~~ ucsc/rbTree.c:576:13: warning: ‘rTreeDump’ defined but not used [-Wunused-function] 576 | static void rTreeDump(struct rbTreeNode *n) | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o ucsc/memalloc.c:357:14: warning: ‘memTrackerRealloc’ defined but not used [-Wunused-function] 357 | static void *memTrackerRealloc(void *vpt, size_t size) | ^~~~~~~~~~~~~~~~~ ucsc/memalloc.c:348:13: warning: ‘memTrackerFree’ defined but not used [-Wunused-function] 348 | static void memTrackerFree(void *vpt) | ^~~~~~~~~~~~~~ ucsc/memalloc.c:314:26: warning: ‘carefulMemHandler’ defined but not used [-Wunused-variable] 314 | static struct memHandler carefulMemHandler = | ^~~~~~~~~~~~~~~~~ ucsc/memalloc.c:220:13: warning: ‘carefulMemInit’ defined but not used [-Wunused-function] 220 | static void carefulMemInit(size_t maxToAlloc) | ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o ucsc/dlist.c:124:12: warning: ‘dlNodeCmp’ defined but not used [-Wunused-function] 124 | static int dlNodeCmp(const void *elem1, const void *elem2) | ^~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/filePath.c -o ucsc/filePath.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/htmlPage.c -o ucsc/htmlPage.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o ucsc/udc.c: In function ‘djb2_hash’: ucsc/udc.c:1070:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1070 | while (c = *str++) | ^ At top level: ucsc/udc.c:1273:13: warning: ‘qDecode’ defined but not used [-Wunused-function] 1273 | static void qDecode(const char *input, char *buf, size_t size) | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o ucsc/net.c: In function ‘netUrlOpenSockets’: ucsc/net.c:155:22: warning: unused variable ‘status’ [-Wunused-variable] 155 | CURLcode status = wrapped_curl_request(curl, GET); | ^~~~~~ ucsc/net.c: In function ‘header_get_last_modified’: ucsc/net.c:29:1: warning: control reaches end of non-void function [-Wreturn-type] 29 | } | ^ ucsc/net.c: In function ‘header_get_content_length’: ucsc/net.c:44:1: warning: control reaches end of non-void function [-Wreturn-type] 44 | } | ^ ucsc/net.c: In function ‘netUrlOpenSockets’: ucsc/net.c:167:1: warning: control reaches end of non-void function [-Wreturn-type] 167 | } | ^ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o ucsc/https.c: In function ‘openSslInit’: ucsc/https.c:76:5: warning: ‘ERR_load_SSL_strings’ is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] 76 | ERR_load_SSL_strings(); | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/openssl/sslerr.h:17, from /usr/include/openssl/ssl.h:43, from ucsc/https.c:8: /usr/include/openssl/sslerr_legacy.h:29:27: note: declared here 29 | OSSL_DEPRECATEDIN_3_0 int ERR_load_SSL_strings(void); | ^~~~~~~~~~~~~~~~~~~~ At top level: ucsc/https.c:27:13: warning: ‘openssl_locking_callback’ defined but not used [-Wunused-function] 27 | static void openssl_locking_callback(int mode, int n, const char * file, int line) | ^~~~~~~~~~~~~~~~~~~~~~~~ ucsc/https.c:22:22: warning: ‘openssl_id_callback’ defined but not used [-Wunused-function] 22 | static unsigned long openssl_id_callback(void) | ^~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.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/filePath.o ucsc/htmlPage.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 -lssl -lcrypto -lcurl -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-rtracklayer/00new/rtracklayer/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’ ** 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 (rtracklayer)