| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 849/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Bohdan Khomtchouk
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | ERROR | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | OK | ERROR | ERROR | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | OK | ERROR | ||||||||||
| See other builds for geneXtendeR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the geneXtendeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geneXtendeR.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: geneXtendeR |
| Version: 1.37.1 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL geneXtendeR |
| StartedAt: 2026-04-16 21:03:37 -0000 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-16 21:03:59 -0000 (Thu, 16 Apr 2026) |
| EllapsedTime: 21.6 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL geneXtendeR
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘geneXtendeR’ ...
** this is package ‘geneXtendeR’ version ‘1.37.1’
** using staged installation
** 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/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c annotate.c -o annotate.o
annotate.c: In function ‘annotate’:
annotate.c:159:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
159 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:191:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
191 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:199:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
199 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:208:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
208 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
annotate.c:228:83: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
228 | Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c extract_number.c -o extract_number.o
extract_number.c: In function ‘extractnumber’:
extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable]
72 | long n_1;
| ^~~
extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable]
66 | long j_1;
| ^~~
extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable]
54 | char * pvcfcol5_5;
| ^~~~~~~~~~
extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable]
53 | char * pvcfcol4_4;
| ^~~~~~~~~~
extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable]
52 | char * pvcfcol3_3;
| ^~~~~~~~~~
extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable]
51 | char * pvcfcol2_2;
| ^~~~~~~~~~
extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable]
50 | char * pvcfcol1_1;
| ^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c extract_peaks.c -o extract_peaks.o
extract_peaks.c: In function ‘extractpeaks’:
extract_peaks.c:202:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
202 | Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
| ~^ ~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-geneXtendeR/00new/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘rtracklayer’:
class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
Execution halted
ERROR: lazy loading failed for package ‘geneXtendeR’
* removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/geneXtendeR’
* restoring previous ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/geneXtendeR’