Back to Multiple platform build/check report for BioC 3.20: simplified long |
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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 check --install=check:beachmat.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings beachmat_2.22.0.tar.gz |
StartedAt: 2024-12-19 20:19:52 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 20:28:24 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 512.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: beachmat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:beachmat.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings beachmat_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/beachmat.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘beachmat/DESCRIPTION’ ... OK * this is package ‘beachmat’ version ‘2.22.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘beachmat’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... NOTE installed size is 105.8Mb sub-directories of 1Mb or more: libs 105.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘DelayedArray:::bplapply2’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed colBlockApply 8.913 1.676 19.671 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/beachmat.Rcheck/00check.log’ for details.
beachmat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL beachmat ### ############################################################################## ############################################################################## * 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)
beachmat.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(beachmat) > test_check("beachmat") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 17538 ] > > proc.time() user system elapsed 64.645 2.148 162.855
beachmat.Rcheck/beachmat-Ex.timings
name | user | system | elapsed | |
checkMemoryCache | 0.415 | 0.001 | 0.417 | |
colBlockApply | 8.913 | 1.676 | 19.671 | |
initializeCpp | 0.013 | 0.000 | 0.013 | |
realizeFileBackedMatrix | 0.417 | 0.028 | 0.445 | |
tatami-utils | 0.006 | 0.000 | 0.006 | |
toCsparse | 0.079 | 0.015 | 0.094 | |
whichNonZero | 0.677 | 0.082 | 0.760 | |