Multiple platform build/check report for BioC 3.20 - INSTALL results for slalom on teran2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4716
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4466
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4498
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4446
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4445
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*

INSTALL results for slalom on teran2

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.

raw results

Summary

Package: slalom

Version: 1.27.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL slalom

StartedAt: 2024-10-02 16:06:15 -0400 (Wed, 02 Oct 2024)

EndedAt: 2024-10-02 16:07:04 -0400 (Wed, 02 Oct 2024)

EllapsedTime: 49.0 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL slalom
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘slalom’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/RcppCommon.h:63,
                 from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 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-3.20-bioc/R/lib -L/usr/local/lib -o slalom.so RcppExports.o slalom-classes.o -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-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)