Multiple platform build/check report for BioC 3.21 - INSTALL results for rtracklayer on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4547
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
INSTALL results for rtracklayer on nebbiolo1

To the developers/maintainers of the rtracklayer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rtracklayer.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: rtracklayer
Version: 1.67.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL rtracklayer
StartedAt: 2025-03-21 15:24:21 -0400 (Fri, 21 Mar 2025)
EndedAt: 2025-03-21 15:25:10 -0400 (Fri, 21 Mar 2025)
EllapsedTime: 49.8 seconds
RetCode: 0
Status: OK
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL rtracklayer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘rtracklayer’ ...
** this is package ‘rtracklayer’ version ‘1.67.1’
** 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 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c readGFF.c -o readGFF.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bbiHelper.c -o bbiHelper.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:268:11: warning: ‘ans_nhits’ may be used uninitialized [-Wmaybe-uninitialized]
  268 |           INTEGER(ans_nhits)[i] = nqhits;
      |           ^~~~~~~~~~~~~~~~~~
bigWig.c:231:58: note: ‘ans_nhits’ was declared here
  231 |   SEXP ans, ans_start, ans_width, ans_score, ans_ranges, ans_nhits;
      |                                                          ^~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bigBedHelper.c -o bigBedHelper.o
In file included from /usr/include/string.h:548,
                 from ucsc/common.h:33,
                 from bigBedHelper.h:5,
                 from bigBedHelper.c:1:
In function ‘strncpy’,
    inlined from ‘bbNamedFileChunkKey’ at bigBedHelper.c:148:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
   95 |   return __builtin___strncpy_chk (__dest, __src, __len,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   96 |                                   __glibc_objsize (__dest));
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bigBed.c -o bigBed.o
bigBed.c: In function ‘BBDFile_query’:
bigBed.c:195:7: warning: ‘name’ may be used uninitialized [-Wmaybe-uninitialized]
  195 |       SET_STRING_ELT(name, i, mkChar(bed->name));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:74:54: note: ‘name’ was declared here
   74 |   SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
      |                                                      ^~~~
bigBed.c:198:7: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized]
  198 |       INTEGER(score)[i] = bed->score;
      |       ^~~~~~~~~~~~~~
bigBed.c:74:60: note: ‘score’ was declared here
   74 |   SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
      |                                                            ^~~~~
bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized [-Wmaybe-uninitialized]
  205 |       INTEGER(thickStart)[i] = bed->thickStart;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:26: note: ‘thickStart’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                          ^~~~~~~~~~
bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized [-Wmaybe-uninitialized]
  204 |       INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
      |       ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:38: note: ‘thickWidth’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                                      ^~~~~~~~~~
bigBed.c:209:7: warning: ‘itemRgb’ may be used uninitialized [-Wmaybe-uninitialized]
  209 |       SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:50: note: ‘itemRgb’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                                                  ^~~~~~~
bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized [-Wmaybe-uninitialized]
  218 |       SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:59: note: ‘blocks’ was declared here
   75 |     strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
      |                                                           ^~~~~~
bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized [-Wmaybe-uninitialized]
  236 |             INTEGER(lengthIndex)[efIndex] = index + 1;
      |             ^~~~~~~~~~~~~~~~~~~~
bigBed.c:76:31: note: ‘lengthIndex’ was declared here
   76 |     extraFields = R_NilValue, lengthIndex;
      |                               ^~~~~~~~~~~
bigBed.c:226:22: warning: ‘typeId’ may be used uninitialized [-Wmaybe-uninitialized]
  226 |         switch(typeId[efIndex]) {
      |                      ^
bigBed.c:141:13: note: ‘typeId’ was declared here
  141 |   SEXPTYPE *typeId;
      |             ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c chain_io.c -o chain_io.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c twoBit.c -o twoBit.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c handlers.c -o handlers.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c utils.c -o utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/memgfx.c -o ucsc/memgfx.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/binRange.c -o ucsc/binRange.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/asParse.c -o ucsc/asParse.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function ‘bedParseRgb’:
ucsc/basicBed.c:449:1: warning: ‘__builtin_strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
  449 | strncpy(dupe, itemRgb, sizeof(dupe));
      | ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bigBed.c -o ucsc/bigBed.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/errAbort.c -o ucsc/errAbort.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/filePath.c -o ucsc/filePath.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘qEncode’:
ucsc/udc.c:936:26: warning: ‘%02X’ directive output may be truncated writing between 2 and 8 bytes into a region of size 2 [-Wformat-truncation=]
  936 |         snprintf(d, 3, "Q%02X", (unsigned)c);
      |                          ^~~~
ucsc/udc.c:936:24: note: directive argument in the range [1, 4294967295]
  936 |         snprintf(d, 3, "Q%02X", (unsigned)c);
      |                        ^~~~~~~
In file included from /usr/include/stdio.h:980,
                 from ucsc/common.h:30,
                 from ucsc/udc.c:34:
In function ‘snprintf’,
    inlined from ‘qEncode’ at ucsc/udc.c:936:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: note: ‘__builtin___snprintf_chk’ output between 4 and 10 bytes into a destination of size 3
   54 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   55 |                                    __glibc_objsize (__s), __fmt,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   56 |                                    __va_arg_pack ());
      |                                    ~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/net.c -o ucsc/net.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-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/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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)