Gabriel Hoffman
| Snapshot Date: 2024-05-15 14:05:05 -0400 (Wed, 15 May 2024) |
| git_url: https://git.bioconductor.org/packages/dreamlet |
| git_branch: devel |
| git_last_commit: cf98b09 |
| git_last_commit_date: 2024-04-30 11:51:18 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-17 11:37:20 -0400 (Fri, 17 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4663 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4398 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4425 |
| 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 590/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dreamlet 1.3.0 (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 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 1.3.0 |
| 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_1.3.0.tar.gz |
| StartedAt: 2024-05-16 00:27:13 -0400 (Thu, 16 May 2024) |
| EndedAt: 2024-05-16 00:39:39 -0400 (Thu, 16 May 2024) |
| EllapsedTime: 746.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dreamlet.Rcheck |
| Warnings: 0 |
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###
### 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_1.3.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/dreamlet.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '1.3.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 85.43 5.64 91.56
fitVarPart 22.89 0.39 23.28
sortCols-method 22.33 0.31 22.64
plotVarPart-methods 22.26 0.36 22.68
plotPercentBars-methods 21.67 0.31 22.33
meta_analysis 18.41 0.49 18.90
stackAssays 11.44 0.28 11.74
run_mash 10.65 0.05 10.75
compositePosteriorTest 9.02 0.08 9.09
aggregateNonCountSignal 7.56 0.65 8.78
plotVolcano-methods 4.86 0.17 5.05
* 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
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###
### 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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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> 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")
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...0.31 secs
CD14+ Monocytes...0.33 secs
CD4 T cells...0.35 secs
CD8 T cells...0.25 secs
FCGR3A+ Monocytes...0.55 secs
B cells...0.19 secs
CD14+ Monocytes...0.37 secs
CD4 T cells...0.23 secs
CD8 T cells...0.14 secs
FCGR3A+ Monocytes...0.41 secs
B cells...0.26 secs
CD14+ Monocytes...0.44 secs
CD4 T cells...0.31 secs
CD8 T cells...0.15 secs
FCGR3A+ Monocytes...0.3 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...0.22 secs
CD14+ Monocytes...0.3 secs
CD4 T cells...0.24 secs
CD8 T cells...0.23 secs
FCGR3A+ Monocytes...0.43 secs
B cells...0.2 secs
CD14+ Monocytes...0.47 secs
CD4 T cells...0.29 secs
CD8 T cells...0.14 secs
FCGR3A+ Monocytes...0.32 secs
B cells...0.28 secs
B cells...0.21 secs
Processing block [[1/1, 1/1]] ... OK
B cells...0.21 secs
CD14+ Monocytes...0.3 secs
CD4 T cells...0.29 secs
CD8 T cells...0.21 secs
FCGR3A+ Monocytes...0.29 secs
B cells...2.7 secs
CD14+ Monocytes...4.1 secs
CD4 T cells...3.9 secs
CD8 T cells...2.4 secs
FCGR3A+ Monocytes...4.1 secs
B cells...0.17 secs
CD14+ Monocytes...0.42 secs
CD4 T cells...0.26 secs
CD8 T cells...0.18 secs
FCGR3A+ Monocytes...0.33 secs
RUNIT TEST PROTOCOL -- Thu May 16 00:39:25 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
69.79 2.98 87.81
dreamlet.Rcheck/dreamlet-Ex.timings
| name | user | system | elapsed | |
| aggregateNonCountSignal | 7.56 | 0.65 | 8.78 | |
| aggregateToPseudoBulk | 1.27 | 0.03 | 1.30 | |
| aggregateVar | 2.38 | 0.03 | 2.41 | |
| as.dreamletResult | 1.20 | 0.03 | 1.22 | |
| buildClusterTreeFromPB | 0.61 | 0.01 | 0.62 | |
| cellCounts | 0.56 | 0.04 | 0.60 | |
| cellTypeSpecificity | 1.96 | 0.07 | 2.03 | |
| checkFormula | 0 | 0 | 0 | |
| coefNames-methods | 2.84 | 0.13 | 2.97 | |
| compositePosteriorTest | 9.02 | 0.08 | 9.09 | |
| computeCellCounts | 0.17 | 0.00 | 0.17 | |
| computeLogCPM | 0.34 | 0.10 | 0.44 | |
| computeNormCounts | 0.22 | 0.03 | 0.25 | |
| details-methods | 2.09 | 0.03 | 2.12 | |
| diffVar-methods | 3.68 | 0.08 | 3.75 | |
| dreamlet | 4.51 | 0.09 | 4.61 | |
| dreamletCompareClusters | 3.13 | 0.03 | 3.16 | |
| dropRedundantTerms | 0 | 0 | 0 | |
| equalFormulas | 0 | 0 | 0 | |
| extractData-methods | 2.44 | 0.05 | 2.49 | |
| fitVarPart | 22.89 | 0.39 | 23.28 | |
| getExprGeneNames | 4.61 | 0.06 | 4.67 | |
| getTreat-methods | 3.00 | 0.15 | 3.18 | |
| meta_analysis | 18.41 | 0.49 | 18.90 | |
| outlier | 0 | 0 | 0 | |
| outlierByAssay | 2.23 | 0.06 | 2.30 | |
| pbWeights | 2.86 | 0.08 | 2.94 | |
| plotBeeswarm | 3.08 | 0.11 | 3.20 | |
| plotCellComposition | 0.97 | 0.03 | 1.00 | |
| plotForest-methods | 3.34 | 0.06 | 3.41 | |
| plotGeneHeatmap-methods | 3.39 | 0.04 | 3.44 | |
| plotHeatmap-methods | 0.89 | 0.04 | 0.92 | |
| plotPCA | 4.58 | 0.09 | 4.67 | |
| plotPercentBars-methods | 21.67 | 0.31 | 22.33 | |
| plotProjection | 1.77 | 0.10 | 1.81 | |
| plotVarPart-methods | 22.26 | 0.36 | 22.68 | |
| plotViolin-methods | 1.10 | 0.06 | 1.15 | |
| plotVolcano-methods | 4.86 | 0.17 | 5.05 | |
| plotVoom-methods | 3.45 | 0.11 | 3.56 | |
| processAssays | 3.20 | 0.08 | 3.28 | |
| removeConstantTerms | 0.02 | 0.00 | 0.02 | |
| residuals-methods | 4.75 | 0.04 | 4.80 | |
| run_mash | 10.65 | 0.05 | 10.75 | |
| seeErrors-methods | 3.66 | 0.11 | 3.76 | |
| sortCols-method | 22.33 | 0.31 | 22.64 | |
| stackAssays | 11.44 | 0.28 | 11.74 | |
| topTable-methods | 3.43 | 0.07 | 3.50 | |
| zenith_gsa-methods | 85.43 | 5.64 | 91.56 | |