| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 608/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dreamlet 1.2.1 (landing page) Gabriel Hoffman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the dreamlet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dreamlet.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: dreamlet |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dreamlet_1.2.1.tar.gz |
| StartedAt: 2024-06-10 14:18:20 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 14:39:20 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 1259.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dreamlet.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dreamlet_1.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.2.1’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 114.124 5.116 180.127
fitVarPart 24.696 0.265 38.390
sortCols-method 21.923 0.221 33.459
plotPercentBars-methods 21.920 0.216 32.470
plotVarPart-methods 21.618 0.209 30.023
meta_analysis 18.877 0.610 29.735
run_mash 14.569 0.150 21.890
compositePosteriorTest 13.919 0.129 20.558
stackAssays 12.801 0.207 20.129
aggregateNonCountSignal 9.022 0.479 14.376
plotBeeswarm 5.655 0.070 8.781
dreamlet 5.033 0.058 7.876
plotVolcano-methods 4.653 0.067 7.092
diffVar-methods 4.440 0.057 6.945
plotPCA 4.107 0.062 6.133
pbWeights 3.840 0.070 6.100
plotGeneHeatmap-methods 3.717 0.044 5.630
getExprGeneNames 3.632 0.070 5.753
plotForest-methods 3.644 0.050 5.584
cellTypeSpecificity 3.579 0.076 5.520
topTable-methods 3.554 0.048 5.635
processAssays 3.534 0.046 5.404
getTreat-methods 3.485 0.047 5.353
plotVoom-methods 3.469 0.063 5.191
residuals-methods 3.443 0.043 5.352
coefNames-methods 3.408 0.051 5.301
seeErrors-methods 3.354 0.040 5.231
as.dreamletResult 3.251 0.049 5.022
* 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
‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck/00check.log’
for details.
dreamlet.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dreamlet
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘dreamlet’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c colsum_beachmat.cpp -o colsum_beachmat.o
In file included from colsum_beachmat.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
^
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
^
8 warnings generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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-apple-darwin20
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)
> 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...0.53 secs
CD14+ Monocytes...0.61 secs
CD4 T cells...0.48 secs
CD8 T cells...0.25 secs
FCGR3A+ Monocytes...0.7 secs
B cells...0.46 secs
CD14+ Monocytes...0.6 secs
CD4 T cells...0.46 secs
CD8 T cells...0.17 secs
FCGR3A+ Monocytes...0.34 secs
B cells...0.45 secs
CD14+ Monocytes...0.69 secs
CD4 T cells...0.43 secs
CD8 T cells...0.27 secs
FCGR3A+ Monocytes...0.53 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...0.26 secs
CD14+ Monocytes...0.45 secs
CD4 T cells...0.41 secs
CD8 T cells...0.31 secs
FCGR3A+ Monocytes...0.57 secs
B cells...0.28 secs
CD14+ Monocytes...0.52 secs
CD4 T cells...0.5 secs
CD8 T cells...0.28 secs
FCGR3A+ Monocytes...0.59 secs
B cells...0.23 secs
B cells...0.26 secs
Processing block [[1/1, 1/1]] ... OK
B cells...0.4 secs
CD14+ Monocytes...0.6 secs
CD4 T cells...0.47 secs
CD8 T cells...0.39 secs
FCGR3A+ Monocytes...0.45 secs
B cells...5.5 secs
CD14+ Monocytes...7.5 secs
CD4 T cells...5.8 secs
CD8 T cells...3.7 secs
FCGR3A+ Monocytes...7.3 secs
B cells...0.31 secs
CD14+ Monocytes...0.54 secs
CD4 T cells...0.32 secs
CD8 T cells...0.19 secs
FCGR3A+ Monocytes...0.37 secs
RUNIT TEST PROTOCOL -- Mon Jun 10 14:38:55 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
81.162 2.424 153.510
dreamlet.Rcheck/dreamlet-Ex.timings
| name | user | system | elapsed | |
| aggregateNonCountSignal | 9.022 | 0.479 | 14.376 | |
| aggregateToPseudoBulk | 1.203 | 0.032 | 1.856 | |
| aggregateVar | 1.380 | 0.029 | 2.165 | |
| as.dreamletResult | 3.251 | 0.049 | 5.022 | |
| buildClusterTreeFromPB | 0.757 | 0.019 | 1.195 | |
| cellCounts | 0.691 | 0.027 | 1.042 | |
| cellTypeSpecificity | 3.579 | 0.076 | 5.520 | |
| checkFormula | 0.000 | 0.000 | 0.003 | |
| coefNames-methods | 3.408 | 0.051 | 5.301 | |
| compositePosteriorTest | 13.919 | 0.129 | 20.558 | |
| computeCellCounts | 0.189 | 0.009 | 0.248 | |
| computeLogCPM | 0.465 | 0.035 | 0.779 | |
| computeNormCounts | 0.322 | 0.019 | 0.498 | |
| details-methods | 2.373 | 0.041 | 3.667 | |
| diffVar-methods | 4.440 | 0.057 | 6.945 | |
| dreamlet | 5.033 | 0.058 | 7.876 | |
| dreamletCompareClusters | 2.991 | 0.054 | 4.723 | |
| dropRedundantTerms | 0.008 | 0.001 | 0.013 | |
| equalFormulas | 0.001 | 0.000 | 0.000 | |
| extractData-methods | 2.426 | 0.039 | 3.801 | |
| fitVarPart | 24.696 | 0.265 | 38.390 | |
| getExprGeneNames | 3.632 | 0.070 | 5.753 | |
| getTreat-methods | 3.485 | 0.047 | 5.353 | |
| meta_analysis | 18.877 | 0.610 | 29.735 | |
| outlier | 0.004 | 0.000 | 0.008 | |
| outlierByAssay | 2.407 | 0.034 | 3.736 | |
| pbWeights | 3.84 | 0.07 | 6.10 | |
| plotBeeswarm | 5.655 | 0.070 | 8.781 | |
| plotCellComposition | 1.135 | 0.026 | 1.722 | |
| plotForest-methods | 3.644 | 0.050 | 5.584 | |
| plotGeneHeatmap-methods | 3.717 | 0.044 | 5.630 | |
| plotHeatmap-methods | 0.839 | 0.017 | 1.305 | |
| plotPCA | 4.107 | 0.062 | 6.133 | |
| plotPercentBars-methods | 21.920 | 0.216 | 32.470 | |
| plotProjection | 2.433 | 0.057 | 3.735 | |
| plotVarPart-methods | 21.618 | 0.209 | 30.023 | |
| plotViolin-methods | 1.084 | 0.022 | 1.372 | |
| plotVolcano-methods | 4.653 | 0.067 | 7.092 | |
| plotVoom-methods | 3.469 | 0.063 | 5.191 | |
| processAssays | 3.534 | 0.046 | 5.404 | |
| removeConstantTerms | 0.006 | 0.000 | 0.013 | |
| residuals-methods | 3.443 | 0.043 | 5.352 | |
| run_mash | 14.569 | 0.150 | 21.890 | |
| seeErrors-methods | 3.354 | 0.040 | 5.231 | |
| sortCols-method | 21.923 | 0.221 | 33.459 | |
| stackAssays | 12.801 | 0.207 | 20.129 | |
| topTable-methods | 3.554 | 0.048 | 5.635 | |
| zenith_gsa-methods | 114.124 | 5.116 | 180.127 | |