Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 598/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dreamlet 1.5.0 (landing page) Gabriel Hoffman
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the dreamlet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dreamlet.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: dreamlet |
Version: 1.5.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings dreamlet_1.5.0.tar.gz |
StartedAt: 2024-12-24 06:17:55 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 06:31:53 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 837.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dreamlet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings dreamlet_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/dreamlet.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dreamlet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dreamlet’ version ‘1.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 36 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘dreamlet’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... OK * 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 ... NOTE checkRd: (-1) meta_analysis.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) meta_analysis.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) meta_analysis.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) outlierByAssay.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly * 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’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed zenith_gsa-methods 106.816 1.768 109.031 sortCols-method 27.479 0.048 27.591 fitVarPart 26.182 0.263 26.506 plotVarPart-methods 25.841 0.175 26.080 plotPercentBars-methods 25.573 0.040 25.672 meta_analysis 23.297 0.168 23.521 stackAssays 14.934 0.111 15.081 run_mash 11.229 0.072 11.327 compositePosteriorTest 9.939 0.190 10.154 aggregateNonCountSignal 8.184 0.416 8.679 plotVolcano-methods 5.501 0.004 5.515 plotForest-methods 5.397 0.103 5.514 diffVar-methods 5.200 0.111 5.324 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/dreamlet.Rcheck/00check.log’ for details.
dreamlet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL dreamlet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘dreamlet’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++11 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c colsum_beachmat.cpp -o colsum_beachmat.o In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/beachmat.h:24, from colsum_beachmat.cpp:1: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 36 | return std::unique_ptr<M>(new integer_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 38 | return std::unique_ptr<M>(new double_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 40 | return std::unique_ptr<M>(new logical_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 596 | return reader.template get_row<const int*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 602 | return reader.template get_row<const double*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 596 | return reader.template get_row<const int*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 602 | return reader.template get_row<const double*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-dreamlet/00new/dreamlet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: variancePartition Loading required namespace: dreamlet *** installing help indices *** copying figures ** 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 (dreamlet)
dreamlet.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(Matrix) > library(dreamlet) Loading required package: variancePartition Loading required package: ggplot2 Loading required package: limma Loading required package: BiocParallel Attaching package: 'variancePartition' The following object is masked from 'package:limma': topTable Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following object is masked from 'package:limma': plotMA The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:Matrix': expand, unname The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > library(DelayedArray) Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep > library(edgeR) Attaching package: 'edgeR' The following object is masked from 'package:SingleCellExperiment': cpm > library(muscat) > library(RUnit) > > BiocGenerics:::testPackage("dreamlet") B cells...0.35 secs B cells...0.28 secs Processing block [[1/1, 1/1]] ... OK B cells...0.3 secs CD14+ Monocytes...0.36 secs CD4 T cells...0.32 secs CD8 T cells...0.21 secs FCGR3A+ Monocytes...0.31 secs B cells...4.6 secs CD14+ Monocytes...6 secs CD4 T cells...4.7 secs CD8 T cells...2.6 secs FCGR3A+ Monocytes...5.8 secs B cells...0.29 secs CD14+ Monocytes...0.46 secs CD4 T cells...0.29 secs CD8 T cells...0.19 secs FCGR3A+ Monocytes...0.35 secs RUNIT TEST PROTOCOL -- Tue Dec 24 06:31:47 2024 *********************************************** Number of test functions: 10 Number of errors: 0 Number of failures: 0 1 Test Suite : dreamlet RUnit Tests - 10 test functions, 0 errors, 0 failures Number of test functions: 10 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 72.707 1.567 93.996
dreamlet.Rcheck/dreamlet-Ex.timings
name | user | system | elapsed | |
aggregateNonCountSignal | 8.184 | 0.416 | 8.679 | |
aggregateToPseudoBulk | 0.897 | 0.036 | 0.935 | |
aggregateVar | 1.304 | 0.020 | 1.327 | |
as.dreamletResult | 1.487 | 0.044 | 1.535 | |
buildClusterTreeFromPB | 1.769 | 0.096 | 1.869 | |
cellCounts | 0.527 | 0.004 | 0.531 | |
cellTypeSpecificity | 3.188 | 0.056 | 3.250 | |
checkFormula | 0 | 0 | 0 | |
coefNames-methods | 3.695 | 0.024 | 3.728 | |
compositePosteriorTest | 9.939 | 0.190 | 10.154 | |
computeCellCounts | 0.183 | 0.000 | 0.183 | |
computeLogCPM | 0.433 | 0.036 | 0.471 | |
computeNormCounts | 0.276 | 0.008 | 0.284 | |
details-methods | 3.439 | 0.060 | 3.506 | |
diffVar-methods | 5.200 | 0.111 | 5.324 | |
dreamlet | 3.839 | 0.076 | 3.923 | |
dreamletCompareClusters | 3.213 | 0.028 | 3.248 | |
dropRedundantTerms | 0.006 | 0.000 | 0.006 | |
equalFormulas | 0 | 0 | 0 | |
extractData-methods | 2.317 | 0.016 | 2.338 | |
fitVarPart | 26.182 | 0.263 | 26.506 | |
getTreat-methods | 3.807 | 0.024 | 3.840 | |
meta_analysis | 23.297 | 0.168 | 23.521 | |
outlier | 0.004 | 0.000 | 0.004 | |
outlierByAssay | 2.333 | 0.040 | 2.378 | |
plotBeeswarm | 4.328 | 0.012 | 4.353 | |
plotCellComposition | 1.167 | 0.020 | 1.190 | |
plotForest-methods | 5.397 | 0.103 | 5.514 | |
plotGeneHeatmap-methods | 4.187 | 0.056 | 4.253 | |
plotHeatmap-methods | 0.836 | 0.004 | 0.841 | |
plotPCA | 4.576 | 0.004 | 4.591 | |
plotPercentBars-methods | 25.573 | 0.040 | 25.672 | |
plotProjection | 2.029 | 0.132 | 2.148 | |
plotVarPart-methods | 25.841 | 0.175 | 26.080 | |
plotViolin-methods | 1.155 | 0.004 | 1.163 | |
plotVolcano-methods | 5.501 | 0.004 | 5.515 | |
plotVoom-methods | 3.533 | 0.012 | 3.553 | |
processAssays | 3.773 | 0.044 | 3.825 | |
removeConstantTerms | 0.006 | 0.000 | 0.006 | |
residuals-methods | 3.841 | 0.012 | 3.862 | |
run_mash | 11.229 | 0.072 | 11.327 | |
seeErrors-methods | 3.750 | 0.012 | 3.770 | |
sortCols-method | 27.479 | 0.048 | 27.591 | |
stackAssays | 14.934 | 0.111 | 15.081 | |
topTable-methods | 3.880 | 0.020 | 3.909 | |
zenith_gsa-methods | 106.816 | 1.768 | 109.031 | |