Aaron Lun
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/beachmat |
| git_branch: RELEASE_3_20 |
| git_last_commit: a143856 |
| git_last_commit_date: 2024-10-29 10:20:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 150/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beachmat 2.22.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: beachmat |
| Version: 2.22.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL beachmat |
| StartedAt: 2024-12-19 15:08:45 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 15:13:15 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 269.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL beachmat
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘beachmat’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/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../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/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/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/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/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/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/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c delayed_other.cpp -o delayed_other.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c dense_matrix.cpp -o dense_matrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/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/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c sparse_matrix.cpp -o sparse_matrix.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/tatami.hpp:8,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami_r/UnknownMatrix.hpp:5,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami_r/tatami_r.hpp:4,
from ../inst/include/Rtatami.h:8,
from sparse_matrix.cpp:1:
/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool, bool) [with Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<int>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:13:12: 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:36:51: required from here
/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp:534:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
534 | for (size_t j = start + 1; j < end; ++j) {
| ~~^~~~~
/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool, bool) [with Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<double>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:13:12: 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:40:54: required from here
/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/tatami/sparse/CompressedSparseMatrix.hpp:534:46: 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/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I/usr/local/include -fpic -g -O2 -Wall -c tatami_utils.cpp -o tatami_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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)