| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 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" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 2118/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Structstrings 1.25.0 (landing page) Felix G.M. Ernst
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the Structstrings package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Structstrings.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: Structstrings |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Structstrings |
| StartedAt: 2025-09-19 20:20:42 -0400 (Fri, 19 Sep 2025) |
| EndedAt: 2025-09-19 20:20:56 -0400 (Fri, 19 Sep 2025) |
| EllapsedTime: 14.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 Structstrings
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* checking for file ‘Structstrings/DESCRIPTION’ ... OK
* preparing ‘Structstrings’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘Structstrings’ ...
** this is package ‘Structstrings’ version ‘1.25.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c DotBracketDataFrame_class.c -o DotBracketDataFrame_class.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:41,
from ../inst/include/Structstrings_defines.h:9,
from Structstrings.h:4,
from DotBracketDataFrame_class.c:1:
DotBracketDataFrame_class.c: In function ‘new_DotBracketDFrame’:
DotBracketDataFrame_class.c:8:17: warning: implicit declaration of function ‘new_DataFrame’; did you mean ‘new_DFrame’? [-Wimplicit-function-declaration]
8 | PROTECT(ans = new_DataFrame("DotBracketDFrame",
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
DotBracketDataFrame_class.c:8:15: warning: assignment to ‘SEXP’ {aka ‘struct SEXPREC *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
8 | PROTECT(ans = new_DataFrame("DotBracketDFrame",
| ^
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_Structstrings.c -o R_init_Structstrings.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o Structstrings.so DotBracketDataFrame_class.o IRanges_stubs.o R_init_Structstrings.o S4Vectors_stubs.o utils.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /tmp/RtmpWiPITh/Rinst3936c956a851d1/00LOCK-Structstrings/00new/Structstrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘Structstrings’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/tmp/RtmpWiPITh/Rinst3936c956a851d1/00LOCK-Structstrings/00new/Structstrings/libs/Structstrings.so':
/tmp/RtmpWiPITh/Rinst3936c956a851d1/00LOCK-Structstrings/00new/Structstrings/libs/Structstrings.so: undefined symbol: new_DataFrame
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/RtmpWiPITh/Rinst3936c956a851d1/Structstrings’
-----------------------------------
ERROR: package installation failed