Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-10-25 11:41:25 -0400 (Wed, 25 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4727 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4465 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4476 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 598/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dreamlet 1.0.0 (landing page) Gabriel Hoffman
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.0.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings dreamlet_1.0.0.tar.gz |
StartedAt: 2023-10-25 10:08:47 -0000 (Wed, 25 Oct 2023) |
EndedAt: 2023-10-25 10:32:21 -0000 (Wed, 25 Oct 2023) |
EllapsedTime: 1414.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dreamlet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings dreamlet_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/dreamlet.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘dreamlet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dreamlet’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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 ‘dreamlet’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 ... OK * checking R 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 ... 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’ ... 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 108.085 2.119 110.579 fitVarPart 26.986 0.188 27.225 sortCols-method 26.801 0.060 26.910 plotVarPart-methods 26.626 0.168 26.845 plotPercentBars-methods 26.420 0.175 26.649 run_mash 13.874 0.163 14.065 aggregateNonCountSignal 8.381 0.383 8.833 plotVolcano-methods 5.692 0.040 5.740 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘cell_covs.Rmd’ using ‘UTF-8’... OK ‘dreamlet.Rmd’ using ‘UTF-8’... OK ‘h5ad_on_disk.Rmd’ using ‘UTF-8’... OK ‘mashr.Rmd’ using ‘UTF-8’... OK ‘non_lin_eff.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/dreamlet.Rcheck/00check.log’ for details.
dreamlet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL dreamlet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘dreamlet’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I/usr/local/include -fPIC -g -O2 -Wall -c colsum_beachmat.cpp -o colsum_beachmat.o In file included from /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/beachmat.h:24, from colsum_beachmat.cpp:1: /home/biocbuild/R/R-4.3.1/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-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:56: 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>]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/R/R-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:56: 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>]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/R/R-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:56: 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>]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here /home/biocbuild/R/R-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/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-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/R/R-4.3.1/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-4.3.1/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-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/R/R-4.3.1/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] /home/biocbuild/R/R-4.3.1/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-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here /home/biocbuild/R/R-4.3.1/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] /home/biocbuild/R/R-4.3.1/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-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/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]’ /home/biocbuild/R/R-4.3.1/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here /home/biocbuild/R/R-4.3.1/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] g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-dreamlet/00new/dreamlet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help 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
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Type 'q()' to quit R. > > library(BiocParallel) > library(DelayedArray) Loading required package: stats4 Loading required package: Matrix Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min 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: 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: 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(Matrix) > library(SingleCellExperiment) Loading required package: SummarizedExperiment Loading required package: GenomicRanges 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:SparseArray': rowMedians The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > library(dreamlet) Loading required package: variancePartition Loading required package: ggplot2 Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Attaching package: 'variancePartition' The following object is masked from 'package:limma': topTable > library(edgeR) Attaching package: 'edgeR' The following object is masked from 'package:SingleCellExperiment': cpm > library(muscat) Warning message: In checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package > library(RUnit) > > BiocGenerics:::testPackage("dreamlet") Warning in .check_arg_assay(x, assay, checkValues) : Assay 'cpm' stores continuous values instead of counts. Make sure this is the intended assay. This dataset contains assays: counts, logcounts, cpm Processing block [[1/1, 1/1]] ... OK B cells...0.46 secs CD14+ Monocytes...0.53 secs CD4 T cells...0.38 secs CD8 T cells...0.27 secs FCGR3A+ Monocytes...0.4 secs B cells...5 secs CD14+ Monocytes...6.4 secs CD4 T cells...5.1 secs CD8 T cells...3 secs FCGR3A+ Monocytes...6 secs B cells...0.23 secs CD14+ Monocytes...0.33 secs CD4 T cells...0.24 secs CD8 T cells...0.15 secs FCGR3A+ Monocytes...0.27 secs RUNIT TEST PROTOCOL -- Wed Oct 25 10:21:36 2023 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : dreamlet RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 63.787 3.611 85.571
dreamlet.Rcheck/dreamlet-Ex.timings
name | user | system | elapsed | |
aggregateNonCountSignal | 8.381 | 0.383 | 8.833 | |
aggregateToPseudoBulk | 1.783 | 0.052 | 1.837 | |
aggregateVar | 1.786 | 0.020 | 1.809 | |
as.dreamletResult | 2.977 | 0.079 | 3.063 | |
buildClusterTreeFromPB | 1.107 | 0.008 | 1.117 | |
cellCounts | 1.014 | 0.016 | 1.032 | |
cellTypeSpecificity | 2.542 | 0.068 | 2.616 | |
checkFormula | 0.001 | 0.000 | 0.001 | |
coefNames-methods | 4.227 | 0.056 | 4.293 | |
computeCellCounts | 0.452 | 0.024 | 0.476 | |
computeLogCPM | 1.771 | 0.124 | 1.898 | |
computeNormCounts | 0.525 | 0.008 | 0.534 | |
details-methods | 3.021 | 0.028 | 3.055 | |
dreamlet | 4.151 | 0.020 | 4.179 | |
dreamletCompareClusters | 3.945 | 0.099 | 4.053 | |
dropRedundantTerms | 0.007 | 0.000 | 0.006 | |
equalFormulas | 0.001 | 0.000 | 0.001 | |
extractData-methods | 3.169 | 0.036 | 3.210 | |
fitVarPart | 26.986 | 0.188 | 27.225 | |
getTreat-methods | 4.196 | 0.036 | 4.241 | |
outlier | 0.009 | 0.000 | 0.010 | |
plotCellComposition | 1.702 | 0.032 | 1.739 | |
plotForest-methods | 4.592 | 0.028 | 4.630 | |
plotGeneHeatmap-methods | 4.598 | 0.028 | 4.635 | |
plotHeatmap-methods | 1.339 | 0.012 | 1.355 | |
plotPercentBars-methods | 26.420 | 0.175 | 26.649 | |
plotProjection | 2.200 | 0.108 | 2.296 | |
plotVarPart-methods | 26.626 | 0.168 | 26.845 | |
plotViolin-methods | 1.690 | 0.008 | 1.702 | |
plotVolcano-methods | 5.692 | 0.040 | 5.740 | |
plotVoom-methods | 4.219 | 0.028 | 4.254 | |
processAssays | 4.119 | 0.012 | 4.138 | |
removeConstantTerms | 0.006 | 0.000 | 0.005 | |
residuals-methods | 4.263 | 0.028 | 4.299 | |
run_mash | 13.874 | 0.163 | 14.065 | |
seeErrors-methods | 4.214 | 0.072 | 4.294 | |
sortCols-method | 26.801 | 0.060 | 26.910 | |
topTable-methods | 4.280 | 0.024 | 4.312 | |
zenith_gsa-methods | 108.085 | 2.119 | 110.579 | |