| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 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" | 4774 |
| 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 355/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chromVAR 1.33.0 (landing page) Alicia Schep
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
|
To the developers/maintainers of the chromVAR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromVAR.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: chromVAR |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data chromVAR |
| StartedAt: 2025-10-31 17:03:43 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 17:04:15 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 32.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data chromVAR
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* checking for file ‘chromVAR/DESCRIPTION’ ... OK
* preparing ‘chromVAR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
-----------------------------------
* installing *source* package ‘chromVAR’ ...
** this is package ‘chromVAR’ version ‘1.33.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pwm_similarity.cpp -o pwm_similarity.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from pwm_similarity.cpp:2:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.cpp -o utils.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from utils.cpp:2:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
utils.cpp: In function ‘Rcpp::NumericVector row_sds(arma::mat&, bool)’:
utils.cpp:12:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
12 | for( int j=0; j < X.n_rows; j++ ) {
| ~~^~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /tmp/RtmpK056ZX/Rinst1ce8b303af42d/00LOCK-chromVAR/00new/chromVAR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘nucleotideSubstitutionMatrix’ is not exported by 'namespace:Biostrings'
Execution halted
ERROR: lazy loading failed for package ‘chromVAR’
* removing ‘/tmp/RtmpK056ZX/Rinst1ce8b303af42d/chromVAR’
-----------------------------------
ERROR: package installation failed