Davis McCarthy
| Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/slalom |
| git_branch: RELEASE_3_22 |
| git_last_commit: 712aadd |
| git_last_commit_date: 2025-10-29 10:41:26 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-30 12:35 -0400 (Thu, 30 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" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 2044/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| slalom 1.32.0 (landing page) Davis McCarthy
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the slalom package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/slalom.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: slalom |
| Version: 1.32.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL slalom |
| StartedAt: 2025-10-29 21:46:15 -0400 (Wed, 29 Oct 2025) |
| EndedAt: 2025-10-29 21:47:14 -0400 (Wed, 29 Oct 2025) |
| EllapsedTime: 58.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL slalom
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘slalom’ ...
** this is package ‘slalom’ version ‘1.32.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c slalom-classes.cpp -o slalom-classes.o
slalom-classes.cpp: In member function ‘void SlalomModel::train()’:
slalom-classes.cpp:223:20: warning: unused variable ‘meanerr’ [-Wunused-variable]
223 | double meanerr = arma::mean(error);
| ^~~~~~~
slalom-classes.cpp:202:12: warning: unused variable ‘meanerr’ [-Wunused-variable]
202 | double meanerr = arma::mean(error);
| ^~~~~~~
slalom-classes.cpp: In member function ‘void SlalomModel::update()’:
slalom-classes.cpp:262:28: warning: ‘void std::random_shuffle(_RAIter, _RAIter, _Generator&&) [with _RAIter = unsigned int*; _Generator = int (&)(int)]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
262 | std::random_shuffle(kunfix.begin(), kunfix.end(), randWrapper);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/functional:67,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include/RcppCommon.h:66,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from slalom-classes.cpp:10:
/usr/include/c++/13/bits/stl_algo.h:4620:5: note: declared here
4620 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~~~~
slalom-classes.cpp: In member function ‘void SlalomModel::updateEpsilon()’:
slalom-classes.cpp:431:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
431 | for (int i = 0; i < this->epsilon_E1.n_elem; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o slalom.so RcppExports.o slalom-classes.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-slalom/00new/slalom/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** 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 (slalom)