Michael Lawrence
| Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/rtracklayer |
| git_branch: devel |
| git_last_commit: 8268289 |
| git_last_commit_date: 2025-09-29 08:29:33 -0400 (Mon, 29 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-02 12:07 -0400 (Thu, 02 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4844 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4576 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 1847/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.69.1 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: rtracklayer |
| Version: 1.69.1 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL rtracklayer |
| StartedAt: 2025-09-29 20:59:04 -0000 (Mon, 29 Sep 2025) |
| EndedAt: 2025-09-29 21:00:15 -0000 (Mon, 29 Sep 2025) |
| EllapsedTime: 71.2 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL rtracklayer
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘rtracklayer’ ...
** this is package ‘rtracklayer’ version ‘1.69.1’
** 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c readGFF.c -o readGFF.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bbiHelper.c -o bbiHelper.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/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;
| ^~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bigBedHelper.c -o bigBedHelper.o
bigBedHelper.c: In function ‘bbNamedFileChunkKey’:
bigBedHelper.c:134:3: warning: ‘strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation]
134 | strncpy(keyBuf,item->name, maxBedNameSize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bigBed.c -o bigBed.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c chain_io.c -o chain_io.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c twoBit.c -o twoBit.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c handlers.c -o handlers.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/memgfx.c -o ucsc/memgfx.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/binRange.c -o ucsc/binRange.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/htmlColor.c -o ucsc/htmlColor.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/sqlList.c -o ucsc/sqlList.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/tokenizer.c -o ucsc/tokenizer.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/asParse.c -o ucsc/asParse.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/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: ‘strncpy’ specified bound 64 equals destination size [-Wstringop-truncation]
449 | strncpy(dupe, itemRgb, sizeof(dupe));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/bigBed.c -o ucsc/bigBed.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/bbiRead.c -o ucsc/bbiRead.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/cirTree.c -o ucsc/cirTree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/common.c -o ucsc/common.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/dnaseq.c -o ucsc/dnaseq.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/dnautil.c -o ucsc/dnautil.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/errAbort.c -o ucsc/errAbort.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/hash.c -o ucsc/hash.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/linefile.c -o ucsc/linefile.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/localmem.c -o ucsc/localmem.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/sqlNum.c -o ucsc/sqlNum.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/zlibFace.c -o ucsc/zlibFace.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/dystring.c -o ucsc/dystring.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/hmmstats.c -o ucsc/hmmstats.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/obscure.c -o ucsc/obscure.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/rangeTree.c -o ucsc/rangeTree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/rbTree.c -o ucsc/rbTree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/memalloc.c -o ucsc/memalloc.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/dlist.c -o ucsc/dlist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/filePath.c -o ucsc/filePath.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/htmlPage.c -o ucsc/htmlPage.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/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:936:30: warning: ‘snprintf’ output truncated before the last format character [-Wformat-truncation=]
936 | snprintf(d, 3, "Q%02X", (unsigned)c);
| ^
ucsc/udc.c:936:9: note: ‘snprintf’ output 4 bytes into a destination of size 3
936 | snprintf(d, 3, "Q%02X", (unsigned)c);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/net.c -o ucsc/net.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/bits.c -o ucsc/bits.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/twoBit.c -o ucsc/twoBit.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/internet.c -o ucsc/internet.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/https.c -o ucsc/https.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/base64.c -o ucsc/base64.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/verbose.c -o ucsc/verbose.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/os.c -o ucsc/os.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/wildcmp.c -o ucsc/wildcmp.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0/site-library/XVector/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ucsc/_portimpl.c -o ucsc/_portimpl.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)