| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-16 11:34 -0500 (Tue, 16 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 | ||||
| Package 1844/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.71.3 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: rtracklayer |
| Version: 1.71.3 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL rtracklayer |
| StartedAt: 2025-12-15 15:26:37 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 15:26:49 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 12.2 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘rtracklayer’ ...
** this is package ‘rtracklayer’ version ‘1.71.3’
** 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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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:134:3:
/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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c bigBed.c -o bigBed.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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:162:15: warning: ‘ourRead’ defined but not used [-Wunused-function]
162 | static size_t ourRead(struct ioStats *ioStats, int fd, void *buf, size_t size)
| ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-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
make: *** No rule to make target 'ucsc/internet.o', needed by 'rtracklayer.so'. Stop.
ERROR: compilation failed for package ‘rtracklayer’
* removing ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/rtracklayer’
* restoring previous ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/rtracklayer’