Gabriel Hoffman
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/dreamlet |
| git_branch: RELEASE_3_18 |
| git_last_commit: 0e59587 |
| git_last_commit_date: 2024-02-27 14:51:44 -0400 (Tue, 27 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:35:55 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1.0.3 (landing page) Gabriel Hoffman
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.0.3 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings dreamlet_1.0.3.tar.gz |
| StartedAt: 2024-03-27 22:05:53 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 22:23:31 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 1058.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dreamlet.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings dreamlet_1.0.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/dreamlet.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.0.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘dreamlet’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 68.735 1.328 70.063
fitVarPart 17.716 0.184 17.899
plotVarPart-methods 17.468 0.052 17.520
sortCols-method 16.354 0.068 16.422
plotPercentBars-methods 16.128 0.108 16.237
meta_analysis 13.934 0.140 14.073
run_mash 9.867 0.116 9.978
stackAssays 9.118 0.016 9.135
compositePosteriorTest 8.604 0.144 8.749
aggregateNonCountSignal 5.675 0.319 6.008
* 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
‘errors.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/bbs-3.18-bioc/R/bin/R CMD INSTALL dreamlet
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘dreamlet’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
from /home/biocbuild/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
from /home/biocbuild/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/beachmat.h:24,
from colsum_beachmat.cpp:1:
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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>]’
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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>]’
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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>]’
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
/home/biocbuild/bbs-3.18-bioc/R/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/bbs-3.18-bioc/R/lib -L/usr/local/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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, sort, 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
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")
Processing: B cells
Computing library sizes...
Processing samples...
Processing: CD14+ Monocytes
Computing library sizes...
Processing samples...
Processing: CD4 T cells
Computing library sizes...
Processing samples...
Processing: CD8 T cells
Computing library sizes...
Processing samples...
Processing: FCGR3A+ Monocytes
Computing library sizes...
Processing samples...
B cells...0.3 secs
CD14+ Monocytes...0.41 secs
CD4 T cells...0.29 secs
CD8 T cells...0.15 secs
FCGR3A+ Monocytes...0.47 secs
B cells...0.24 secs
CD14+ Monocytes...0.41 secs
CD4 T cells...0.31 secs
CD8 T cells...0.15 secs
FCGR3A+ Monocytes...0.36 secs
B cells...0.23 secs
CD14+ Monocytes...0.41 secs
CD4 T cells...0.29 secs
CD8 T cells...0.17 secs
FCGR3A+ Monocytes...0.36 secs
Processing: B cells
Computing library sizes...
Processing samples...
Processing: CD14+ Monocytes
Computing library sizes...
Processing samples...
Processing: CD4 T cells
Computing library sizes...
Processing samples...
Processing: CD8 T cells
Computing library sizes...
Processing samples...
Processing: FCGR3A+ Monocytes
Computing library sizes...
Processing samples...
B cells...0.24 secs
CD14+ Monocytes...0.38 secs
CD4 T cells...0.28 secs
CD8 T cells...0.15 secs
FCGR3A+ Monocytes...0.46 secs
B cells...0.23 secs
CD14+ Monocytes...0.42 secs
CD4 T cells...0.27 secs
CD8 T cells...0.14 secs
FCGR3A+ Monocytes...0.36 secs
B cells...0.23 secs
B cells...0.24 secs
Processing block [[1/1, 1/1]] ... OK
B cells...0.27 secs
CD14+ Monocytes...0.35 secs
CD4 T cells...0.36 secs
CD8 T cells...0.18 secs
FCGR3A+ Monocytes...0.28 secs
B cells...3 secs
CD14+ Monocytes...5.1 secs
CD4 T cells...3 secs
CD8 T cells...1.7 secs
FCGR3A+ Monocytes...3.6 secs
B cells...0.12 secs
CD14+ Monocytes...0.18 secs
CD4 T cells...0.13 secs
CD8 T cells...0.083 secs
FCGR3A+ Monocytes...0.16 secs
RUNIT TEST PROTOCOL -- Wed Mar 27 22:15:56 2024
***********************************************
Number of test functions: 12
Number of errors: 0
Number of failures: 0
1 Test Suite :
dreamlet RUnit Tests - 12 test functions, 0 errors, 0 failures
Number of test functions: 12
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
61.756 2.415 77.956
dreamlet.Rcheck/dreamlet-Ex.timings
| name | user | system | elapsed | |
| aggregateNonCountSignal | 5.675 | 0.319 | 6.008 | |
| aggregateToPseudoBulk | 0.978 | 0.020 | 0.998 | |
| aggregateVar | 1.031 | 0.012 | 1.044 | |
| as.dreamletResult | 2.086 | 0.128 | 2.213 | |
| buildClusterTreeFromPB | 0.588 | 0.016 | 0.605 | |
| cellCounts | 0.55 | 0.02 | 0.57 | |
| cellTypeSpecificity | 2.382 | 0.107 | 2.490 | |
| checkFormula | 0.001 | 0.000 | 0.000 | |
| coefNames-methods | 2.591 | 0.060 | 2.651 | |
| compositePosteriorTest | 8.604 | 0.144 | 8.749 | |
| computeCellCounts | 0.165 | 0.008 | 0.173 | |
| computeLogCPM | 0.343 | 0.064 | 0.407 | |
| computeNormCounts | 0.235 | 0.008 | 0.243 | |
| details-methods | 2.026 | 0.040 | 2.066 | |
| diffVar-methods | 3.206 | 0.080 | 3.286 | |
| dreamlet | 3.616 | 0.016 | 3.632 | |
| dreamletCompareClusters | 2.206 | 0.016 | 2.222 | |
| dropRedundantTerms | 0.005 | 0.000 | 0.005 | |
| equalFormulas | 0 | 0 | 0 | |
| extractData-methods | 2.113 | 0.012 | 2.126 | |
| fitVarPart | 17.716 | 0.184 | 17.899 | |
| getExprGeneNames | 2.898 | 0.040 | 2.938 | |
| getTreat-methods | 2.643 | 0.024 | 2.667 | |
| meta_analysis | 13.934 | 0.140 | 14.073 | |
| outlier | 0.000 | 0.002 | 0.003 | |
| outlierByAssay | 2.058 | 0.024 | 2.081 | |
| pbWeights | 2.939 | 0.044 | 2.984 | |
| plotBeeswarm | 3.938 | 0.140 | 4.077 | |
| plotCellComposition | 0.95 | 0.02 | 0.97 | |
| plotForest-methods | 2.793 | 0.032 | 2.826 | |
| plotGeneHeatmap-methods | 2.872 | 0.032 | 2.904 | |
| plotHeatmap-methods | 0.741 | 0.004 | 0.744 | |
| plotPCA | 3.095 | 0.020 | 3.115 | |
| plotPercentBars-methods | 16.128 | 0.108 | 16.237 | |
| plotProjection | 1.586 | 0.143 | 1.689 | |
| plotVarPart-methods | 17.468 | 0.052 | 17.520 | |
| plotViolin-methods | 0.939 | 0.028 | 0.968 | |
| plotVolcano-methods | 3.829 | 0.012 | 3.825 | |
| plotVoom-methods | 2.907 | 0.004 | 2.912 | |
| processAssays | 2.654 | 0.020 | 2.675 | |
| removeConstantTerms | 0.004 | 0.000 | 0.004 | |
| residuals-methods | 2.660 | 0.008 | 2.668 | |
| run_mash | 9.867 | 0.116 | 9.978 | |
| seeErrors-methods | 2.656 | 0.072 | 2.728 | |
| sortCols-method | 16.354 | 0.068 | 16.422 | |
| stackAssays | 9.118 | 0.016 | 9.135 | |
| topTable-methods | 2.717 | 0.020 | 2.737 | |
| zenith_gsa-methods | 68.735 | 1.328 | 70.063 | |