| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-04 11:44 -0400 (Thu, 04 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" | 4411 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4413 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4395 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
| 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 593/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dreamlet 1.3.1 (landing page) Gabriel Hoffman
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 1.3.1 |
| 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_1.3.1.tar.gz |
| StartedAt: 2024-07-04 04:36:15 -0000 (Thu, 04 Jul 2024) |
| EndedAt: 2024-07-04 04:50:16 -0000 (Thu, 04 Jul 2024) |
| EllapsedTime: 840.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: dreamlet.Rcheck |
| Warnings: NA |
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### 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_1.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/dreamlet.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.3.1’
* 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 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 109.452 1.839 111.532
fitVarPart 26.712 0.184 26.947
plotVarPart-methods 26.525 0.268 26.849
plotPercentBars-methods 26.004 0.310 26.372
sortCols-method 26.053 0.128 26.237
meta_analysis 22.126 0.511 22.688
stackAssays 14.576 0.032 14.640
run_mash 11.705 0.144 11.875
compositePosteriorTest 10.706 0.120 10.849
aggregateNonCountSignal 8.886 0.252 9.207
plotVolcano-methods 5.533 0.064 5.607
diffVar-methods 5.389 0.072 5.470
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error: 'block' is not a recognized matrix representation
Test files with failing tests
test_pseudobulk.R
test_colsum_fast
Error in BiocGenerics:::testPackage("dreamlet") :
unit tests failed for package dreamlet
Execution halted
* 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: 1 ERROR, 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/dreamlet.Rcheck/00check.log’
for details.
dreamlet.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL dreamlet
###
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* installing to library ‘/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
from /home/biocbuild/R/R-4.4.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
from /home/biocbuild/R/R-4.4.0/site-library/beachmat/include/beachmat3/beachmat.h:24,
from colsum_beachmat.cpp:1:
/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63: required from here
/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here
/home/biocbuild/R/R-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/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-4.4.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here
/home/biocbuild/R/R-4.4.0/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-4.4.0/lib -L/usr/local/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -L/home/biocbuild/R/R-4.4.0/lib -lR
installing to /home/biocbuild/R/R-4.4.0/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 4.4.0 (2024-04-24) -- "Puppy Cup"
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
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
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)
Warning message:
In checkDepPackageVersion(dep_pkg = "TMB") :
Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.11
Current TMB version is 1.9.13
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
> library(RUnit)
>
> BiocGenerics:::testPackage("dreamlet")
B cells...0.37 secs
B cells...0.29 secs
Processing block [[1/1, 1/1]] ... OK
B cells...0.28 secs
CD14+ Monocytes...0.36 secs
CD4 T cells...0.32 secs
CD8 T cells...0.23 secs
FCGR3A+ Monocytes...0.32 secs
B cells...4.5 secs
CD14+ Monocytes...6.1 secs
CD4 T cells...4.9 secs
CD8 T cells...2.9 secs
FCGR3A+ Monocytes...5.7 secs
B cells...0.29 secs
CD14+ Monocytes...0.46 secs
CD4 T cells...0.29 secs
CD8 T cells...0.18 secs
FCGR3A+ Monocytes...0.35 secs
RUNIT TEST PROTOCOL -- Wed Jul 3 04:50:53 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
73.110 1.488 93.779
dreamlet.Rcheck/tests/runTests.Rout.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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
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
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)
Warning message:
In checkDepPackageVersion(dep_pkg = "TMB") :
Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.11
Current TMB version is 1.9.14
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
> library(RUnit)
>
> BiocGenerics:::testPackage("dreamlet")
B cells...0.37 secs
B cells...0.29 secs
Processing block [[1/1, 1/1]] ... OK
B cells...0.3 secs
CD14+ Monocytes...0.38 secs
CD4 T cells...0.34 secs
CD8 T cells...0.27 secs
FCGR3A+ Monocytes...0.34 secs
B cells...4.9 secs
CD14+ Monocytes...6.5 secs
CD4 T cells...5 secs
CD8 T cells...2.9 secs
FCGR3A+ Monocytes...6.1 secs
B cells...0.3 secs
CD14+ Monocytes...0.47 secs
CD4 T cells...0.3 secs
CD8 T cells...0.19 secs
FCGR3A+ Monocytes...0.38 secs
Timing stopped at: 0.082 0.008 0.09
Error : BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error: 'block' is not a recognized matrix representation
RUNIT TEST PROTOCOL -- Thu Jul 4 04:50:11 2024
***********************************************
Number of test functions: 10
Number of errors: 1
Number of failures: 0
1 Test Suite :
dreamlet RUnit Tests - 10 test functions, 1 error, 0 failures
ERROR in test_colsum_fast: Error : BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error: 'block' is not a recognized matrix representation
Test files with failing tests
test_pseudobulk.R
test_colsum_fast
Error in BiocGenerics:::testPackage("dreamlet") :
unit tests failed for package dreamlet
Execution halted
dreamlet.Rcheck/dreamlet-Ex.timings
| name | user | system | elapsed | |
| aggregateNonCountSignal | 8.886 | 0.252 | 9.207 | |
| aggregateToPseudoBulk | 1.461 | 0.047 | 1.531 | |
| aggregateVar | 1.586 | 0.036 | 1.626 | |
| as.dreamletResult | 2.978 | 0.076 | 3.060 | |
| buildClusterTreeFromPB | 0.848 | 0.008 | 0.857 | |
| cellCounts | 0.712 | 0.016 | 0.729 | |
| cellTypeSpecificity | 2.224 | 0.055 | 2.283 | |
| checkFormula | 0 | 0 | 0 | |
| coefNames-methods | 4.020 | 0.014 | 4.044 | |
| compositePosteriorTest | 10.706 | 0.120 | 10.849 | |
| computeCellCounts | 0.185 | 0.000 | 0.186 | |
| computeLogCPM | 1.634 | 0.000 | 1.637 | |
| computeNormCounts | 0.272 | 0.012 | 0.284 | |
| details-methods | 2.491 | 0.048 | 2.544 | |
| diffVar-methods | 5.389 | 0.072 | 5.470 | |
| dreamlet | 3.965 | 0.012 | 3.983 | |
| dreamletCompareClusters | 3.448 | 0.028 | 3.483 | |
| dropRedundantTerms | 0.003 | 0.004 | 0.006 | |
| equalFormulas | 0.001 | 0.000 | 0.000 | |
| extractData-methods | 2.546 | 0.004 | 2.554 | |
| fitVarPart | 26.712 | 0.184 | 26.947 | |
| getTreat-methods | 4.044 | 0.034 | 4.088 | |
| meta_analysis | 22.126 | 0.511 | 22.688 | |
| outlier | 0.004 | 0.000 | 0.004 | |
| outlierByAssay | 2.592 | 0.120 | 2.718 | |
| plotBeeswarm | 4.581 | 0.140 | 4.732 | |
| plotCellComposition | 1.282 | 0.056 | 1.342 | |
| plotForest-methods | 4.344 | 0.139 | 4.495 | |
| plotGeneHeatmap-methods | 4.392 | 0.095 | 4.497 | |
| plotHeatmap-methods | 1.078 | 0.004 | 1.084 | |
| plotPCA | 4.767 | 0.136 | 4.914 | |
| plotPercentBars-methods | 26.004 | 0.310 | 26.372 | |
| plotProjection | 2.013 | 0.132 | 2.131 | |
| plotVarPart-methods | 26.525 | 0.268 | 26.849 | |
| plotViolin-methods | 1.393 | 0.039 | 1.437 | |
| plotVolcano-methods | 5.533 | 0.064 | 5.607 | |
| plotVoom-methods | 3.663 | 0.016 | 3.687 | |
| processAssays | 4.045 | 0.004 | 4.058 | |
| removeConstantTerms | 0.005 | 0.000 | 0.005 | |
| residuals-methods | 4.034 | 0.024 | 4.067 | |
| run_mash | 11.705 | 0.144 | 11.875 | |
| seeErrors-methods | 3.858 | 0.044 | 3.910 | |
| sortCols-method | 26.053 | 0.128 | 26.237 | |
| stackAssays | 14.576 | 0.032 | 14.640 | |
| topTable-methods | 4.033 | 0.019 | 4.061 | |
| zenith_gsa-methods | 109.452 | 1.839 | 111.532 | |