Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-30 11:40 -0400 (Tue, 30 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4690 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4387 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4406 |
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 596/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dreamlet 1.3.3 (landing page) Gabriel Hoffman
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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. |
Package: dreamlet |
Version: 1.3.3 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dreamlet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings dreamlet_1.3.3.tar.gz |
StartedAt: 2024-07-30 00:36:17 -0400 (Tue, 30 Jul 2024) |
EndedAt: 2024-07-30 00:49:21 -0400 (Tue, 30 Jul 2024) |
EllapsedTime: 784.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dreamlet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dreamlet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings dreamlet_1.3.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/dreamlet.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'dreamlet/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'dreamlet' version '1.3.3' * 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 whether package 'dreamlet' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... 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 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/dreamlet/libs/x64/dreamlet.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 97.64 4.94 102.67 plotPercentBars-methods 23.67 0.36 24.07 plotVarPart-methods 23.54 0.47 24.03 sortCols-method 23.65 0.36 24.14 fitVarPart 23.25 0.37 23.63 meta_analysis 20.64 0.56 21.20 stackAssays 14.19 0.17 14.36 run_mash 11.31 0.11 11.42 compositePosteriorTest 9.61 0.06 9.69 aggregateNonCountSignal 8.19 0.59 9.66 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/dreamlet.Rcheck/00check.log' for details.
dreamlet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL dreamlet ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'dreamlet' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c colsum_beachmat.cpp -o colsum_beachmat.o In file included from F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12, from F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from colsum_beachmat.cpp:1: F:/biocbuild/bbs-3.20-bioc/R/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>]': F:/biocbuild/bbs-3.20-bioc/R/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>]' F:/biocbuild/bbs-3.20-bioc/R/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>]' F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ F:/biocbuild/bbs-3.20-bioc/R/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>]': F:/biocbuild/bbs-3.20-bioc/R/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>]' F:/biocbuild/bbs-3.20-bioc/R/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>]' F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ F:/biocbuild/bbs-3.20-bioc/R/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>]': F:/biocbuild/bbs-3.20-bioc/R/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>]' F:/biocbuild/bbs-3.20-bioc/R/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>]' F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int; size_t = long long unsigned int]': F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int; size_t = long long unsigned int]': F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int; size_t = long long unsigned int]': F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int; size_t = long long unsigned int]': F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/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 long unsigned int]' F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here F:/biocbuild/bbs-3.20-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] g++ -shared -s -static-libgcc -o dreamlet.dll tmp.def RcppExports.o colsum_beachmat.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-dreamlet/00new/dreamlet/libs/x64 ** 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 ** 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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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...0.31 secs B cells...0.27 secs Processing block [[1/1, 1/1]] ... OK B cells...0.21 secs CD14+ Monocytes...0.36 secs CD4 T cells...0.3 secs CD8 T cells...0.23 secs FCGR3A+ Monocytes...0.23 secs B cells...4.1 secs CD14+ Monocytes...5.3 secs CD4 T cells...4.6 secs CD8 T cells...2.6 secs FCGR3A+ Monocytes...5.1 secs B cells...0.17 secs CD14+ Monocytes...0.42 secs CD4 T cells...0.29 secs CD8 T cells...0.14 secs FCGR3A+ Monocytes...0.26 secs RUNIT TEST PROTOCOL -- Tue Jul 30 00:49:09 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 65.23 2.79 84.67
dreamlet.Rcheck/dreamlet-Ex.timings
name | user | system | elapsed | |
aggregateNonCountSignal | 8.19 | 0.59 | 9.66 | |
aggregateToPseudoBulk | 1.19 | 0.03 | 1.22 | |
aggregateVar | 1.31 | 0.03 | 1.35 | |
as.dreamletResult | 2.85 | 0.08 | 2.92 | |
buildClusterTreeFromPB | 0.83 | 0.02 | 0.84 | |
cellCounts | 0.78 | 0.00 | 0.78 | |
cellTypeSpecificity | 2.06 | 0.08 | 2.14 | |
checkFormula | 0 | 0 | 0 | |
coefNames-methods | 3.48 | 0.11 | 3.61 | |
compositePosteriorTest | 9.61 | 0.06 | 9.69 | |
computeCellCounts | 0.18 | 0.02 | 0.19 | |
computeLogCPM | 1.65 | 0.12 | 1.78 | |
computeNormCounts | 0.22 | 0.05 | 0.27 | |
details-methods | 2.15 | 0.04 | 2.21 | |
diffVar-methods | 4.86 | 0.11 | 4.96 | |
dreamlet | 3.33 | 0.08 | 3.41 | |
dreamletCompareClusters | 2.88 | 0.14 | 3.02 | |
dropRedundantTerms | 0 | 0 | 0 | |
equalFormulas | 0 | 0 | 0 | |
extractData-methods | 2.41 | 0.10 | 2.52 | |
fitVarPart | 23.25 | 0.37 | 23.63 | |
getTreat-methods | 3.47 | 0.14 | 3.61 | |
meta_analysis | 20.64 | 0.56 | 21.20 | |
outlier | 0 | 0 | 0 | |
outlierByAssay | 2.33 | 0.05 | 2.38 | |
plotBeeswarm | 4.09 | 0.13 | 4.23 | |
plotCellComposition | 1.16 | 0.06 | 1.22 | |
plotForest-methods | 3.88 | 0.11 | 3.98 | |
plotGeneHeatmap-methods | 3.64 | 0.11 | 3.75 | |
plotHeatmap-methods | 0.84 | 0.01 | 0.86 | |
plotPCA | 4.44 | 0.10 | 4.53 | |
plotPercentBars-methods | 23.67 | 0.36 | 24.07 | |
plotProjection | 0.81 | 0.07 | 0.82 | |
plotVarPart-methods | 23.54 | 0.47 | 24.03 | |
plotViolin-methods | 1.37 | 0.03 | 1.40 | |
plotVolcano-methods | 4.77 | 0.11 | 4.88 | |
plotVoom-methods | 3.62 | 0.08 | 3.71 | |
processAssays | 3.18 | 0.05 | 3.24 | |
removeConstantTerms | 0 | 0 | 0 | |
residuals-methods | 3.25 | 0.08 | 3.33 | |
run_mash | 11.31 | 0.11 | 11.42 | |
seeErrors-methods | 3.71 | 0.18 | 3.89 | |
sortCols-method | 23.65 | 0.36 | 24.14 | |
stackAssays | 14.19 | 0.17 | 14.36 | |
topTable-methods | 3.81 | 0.10 | 3.91 | |
zenith_gsa-methods | 97.64 | 4.94 | 102.67 | |