############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rtracklayer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/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-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c readGFF.c -o readGFF.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bbiHelper.c -o bbiHelper.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigBedHelper.c -o bigBedHelper.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/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-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c chain_io.c -o chain_io.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c handlers.c -o handlers.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/memgfx.c -o ucsc/memgfx.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/aliType.c -o ucsc/aliType.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/binRange.c -o ucsc/binRange.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/htmlColor.c -o ucsc/htmlColor.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/tokenizer.c -o ucsc/tokenizer.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/asParse.c -o ucsc/asParse.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/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:495, from ucsc/common.h:33, from ucsc/basicBed.c:14: In function ‘strncpy’, inlined from ‘bedParseRgb’ at ucsc/basicBed.c:997:1: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bigBed.c -o ucsc/bigBed.o ucsc/bigBed.c: In function ‘extractField’: ucsc/bigBed.c:314:2: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 314 | warn("Not enough fields in extractField of %s", line); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/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:187:18: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable] 187 | char *blockPt, *blockEnd; | ^~~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/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:331:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 331 | write(STDERR_FILENO, errMsg, strlen(errMsg)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hex.c -o ucsc/hex.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/filePath.c -o ucsc/filePath.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/htmlPage.c -o ucsc/htmlPage.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o In file included from ucsc/udc.c:41: ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment] 178 | /* Use byteRange as a work-around alternate method to get file size (content-length). | gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o In file included from ucsc/net.c:19: ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment] 178 | /* Use byteRange as a work-around alternate method to get file size (content-length). | ucsc/net.c: In function ‘netConnectWithTimeout’: ucsc/net.c:148:31: warning: passing argument 3 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] 148 | res = select(sd+1, NULL, &mySet, &mySet, &tempTime); | ^~~~~~ ~~~~~~ gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o In file included from ucsc/twoBit.c:15: ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment] 178 | /* Use byteRange as a work-around alternate method to get file size (content-length). | gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o In file included from ucsc/https.c:17: ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment] 178 | /* Use byteRange as a work-around alternate method to get file size (content-length). | 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-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.14-bioc/R/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-3.14-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/aliType.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/hex.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 -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/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)