Aaron Lun
| Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/beachmat |
| git_branch: devel |
| git_last_commit: bbbd414 |
| git_last_commit_date: 2024-03-28 10:15:25 -0400 (Thu, 28 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-04-29 11:40:33 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 146/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beachmat 2.19.4 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the beachmat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beachmat.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: beachmat |
| Version: 2.19.4 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL beachmat |
| StartedAt: 2024-04-28 19:12:50 -0000 (Sun, 28 Apr 2024) |
| EndedAt: 2024-04-28 19:21:31 -0000 (Sun, 28 Apr 2024) |
| EllapsedTime: 520.2 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL beachmat
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘beachmat’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c delayed_isometric_math.cpp -o delayed_isometric_math.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c delayed_other.cpp -o delayed_other.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c dense_matrix.cpp -o dense_matrix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c sparse_matrix.cpp -o sparse_matrix.o
In file included from ../inst/include/tatami/tatami.hpp:6,
from ../inst/include/tatami_r/UnknownMatrix.hpp:5,
from ../inst/include/tatami_r/tatami_r.hpp:4,
from ../inst/include/Rtatami.h:8,
from sparse_matrix.cpp:1:
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<row_, Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool) [with bool row_ = true; Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<int>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:15:16: required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = int; XVector_ = Rcpp::Vector<10, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix<double, int>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
sparse_matrix.cpp:39:111: required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
112 | for (size_t j = start + 1; j < end; ++j) {
| ~~^~~~~
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<row_, Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool) [with bool row_ = false; Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<int>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:18:16: required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = int; XVector_ = Rcpp::Vector<10, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix<double, int>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
sparse_matrix.cpp:39:111: required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<row_, Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool) [with bool row_ = true; Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<double>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:15:16: required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = double; XVector_ = Rcpp::Vector<14, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix<double, int>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
sparse_matrix.cpp:42:114: required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<row_, Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool) [with bool row_ = false; Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<double>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:18:16: required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = double; XVector_ = Rcpp::Vector<14, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix<double, int>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
sparse_matrix.cpp:42:114: required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c tatami_utils.cpp -o tatami_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c unknown_matrix.cpp -o unknown_matrix.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o beachmat.so RcppExports.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o sparse_matrix.o tatami_utils.o unknown_matrix.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-beachmat/00new/beachmat/libs
** R
** 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 (beachmat)