Michael Lawrence
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/rtracklayer |
| Branch: RELEASE_3_12 |
| Last Commit: d2e61f7 |
| Last Changed Date: 2020-10-27 10:33:14 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:56 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the rtracklayer package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1598/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.50.0 (landing page) Michael Lawrence
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: rtracklayer |
| Version: 1.50.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL rtracklayer |
| StartedAt: 2021-05-05 16:32:30 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 16:33:25 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 55.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c readGFF.c -o readGFF.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bbiHelper.c -o bbiHelper.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:268:4: warning: ‘ans_nhits’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(ans_nhits)[i] = nqhits;
^~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c bigBedHelper.c -o bigBedHelper.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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]
bits64 extraIndexListEndOffset = 0;
^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function ‘BBDFile_query’:
bigBed.c:226:22: warning: ‘typeId’ may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(typeId[efIndex]) {
^
bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(lengthIndex)[efIndex] = index + 1;
^~~~~~~~~~~~~~~~~~~~
bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized in this function [-Wmaybe-uninitialized]
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]
SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
^~~~~~~~~~~~~~~~~~~
bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(thickStart)[i] = bed->thickStart;
^~~~~~~~~~~~~~~~~~~
bigBed.c:198:7: warning: ‘score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(score)[i] = bed->score;
^~~~~~~~~~~~~~
bigBed.c:257:5: warning: ‘name’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans, index++, name);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c handlers.c -o handlers.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/basicBed.c -o ucsc/basicBed.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bigBed.c -o ucsc/bigBed.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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]
char *blockPt, *blockEnd;
^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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]
write(STDERR_FILENO, errMsg, strlen(errMsg));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
ucsc/https.c:27:13: warning: ‘openssl_locking_callback’ defined but not used [-Wunused-function]
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]
static unsigned long openssl_id_callback(void)
^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-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/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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)