Back to Multiple platform build/check report for BioC 3.18:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-04-17 11:36:33 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 144/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beachmat 2.18.1  (landing page)
Aaron Lun
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/beachmat
git_branch: RELEASE_3_18
git_last_commit: 39ef12f
git_last_commit_date: 2024-01-22 13:40:03 -0400 (Mon, 22 Jan 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for beachmat on palomino4


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.

raw results

Summary

Package: beachmat
Version: 2.18.1
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL beachmat
StartedAt: 2024-04-15 15:45:56 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 15:53:32 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 455.9 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL beachmat
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'beachmat' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++17
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c delayed_isometric_math.cpp -o delayed_isometric_math.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c delayed_other.cpp -o delayed_other.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dense_matrix.cpp -o dense_matrix.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:39:51:   required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long 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:39:51:   required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long 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:42:54:   required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long 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:42:54:   required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:112:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tatami_utils.cpp -o tatami_utils.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c unknown_matrix.cpp -o unknown_matrix.o
g++ -shared -s -static-libgcc -o beachmat.dll tmp.def 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 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-beachmat/00new/beachmat/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beachmat)