| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.6.6 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: 2024-10-17 04:34:31 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 05:04:50 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 1819.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dreamlet.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 178.449 9.649 228.207
fitVarPart 48.265 0.445 61.203
plotVarPart-methods 46.354 0.390 56.939
sortCols-method 46.111 0.381 56.452
plotPercentBars-methods 45.596 0.331 56.200
meta_analysis 36.960 0.567 47.060
stackAssays 25.958 0.227 31.694
aggregateNonCountSignal 14.838 0.907 20.102
run_mash 14.689 0.214 17.550
compositePosteriorTest 12.869 0.184 16.757
diffVar-methods 10.582 0.119 13.250
plotVolcano-methods 10.365 0.133 12.664
plotBeeswarm 9.553 0.115 11.920
plotGeneHeatmap-methods 9.352 0.102 11.466
plotPCA 8.896 0.086 10.962
dreamlet 8.848 0.106 11.173
plotForest-methods 8.108 0.071 9.932
residuals-methods 7.673 0.084 9.301
getTreat-methods 7.643 0.073 9.498
topTable-methods 7.597 0.063 9.008
seeErrors-methods 7.550 0.096 9.316
coefNames-methods 7.549 0.086 9.355
processAssays 7.553 0.068 9.109
pbWeights 6.653 0.105 8.581
getExprGeneNames 6.640 0.091 8.184
plotVoom-methods 6.503 0.075 7.847
dreamletCompareClusters 6.383 0.092 7.736
extractData-methods 4.600 0.058 5.740
outlierByAssay 4.534 0.050 5.630
details-methods 4.357 0.079 5.539
cellTypeSpecificity 3.991 0.134 5.105
* 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
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dreamlet
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘dreamlet’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/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-x86_64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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-x86_64/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 x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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...0.83 secs
CD14+ Monocytes...1 secs
CD4 T cells...0.8 secs
CD8 T cells...0.56 secs
FCGR3A+ Monocytes...1.3 secs
B cells...0.61 secs
CD14+ Monocytes...0.96 secs
CD4 T cells...0.71 secs
CD8 T cells...0.45 secs
FCGR3A+ Monocytes...0.94 secs
B cells...0.67 secs
CD14+ Monocytes...1.1 secs
CD4 T cells...0.85 secs
CD8 T cells...0.51 secs
FCGR3A+ Monocytes...0.89 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...0.63 secs
CD14+ Monocytes...0.93 secs
CD4 T cells...0.75 secs
CD8 T cells...0.53 secs
FCGR3A+ Monocytes...2.6 secs
B cells...0.61 secs
CD14+ Monocytes...0.97 secs
CD4 T cells...0.71 secs
CD8 T cells...0.45 secs
FCGR3A+ Monocytes...0.89 secs
B cells...0.68 secs
B cells...0.62 secs
Processing block [[1/1, 1/1]] ... OK
B cells...0.62 secs
CD14+ Monocytes...0.76 secs
CD4 T cells...0.72 secs
CD8 T cells...0.49 secs
FCGR3A+ Monocytes...0.76 secs
B cells...10 secs
CD14+ Monocytes...14 secs
CD4 T cells...11 secs
CD8 T cells...6.6 secs
FCGR3A+ Monocytes...17 secs
B cells...1.3 secs
CD14+ Monocytes...1.4 secs
CD4 T cells...1.2 secs
CD8 T cells...0.45 secs
FCGR3A+ Monocytes...1.2 secs
RUNIT TEST PROTOCOL -- Thu Oct 17 05:04:00 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
147.052 4.946 234.508
dreamlet.Rcheck/dreamlet-Ex.timings
| name | user | system | elapsed | |
| aggregateNonCountSignal | 14.838 | 0.907 | 20.102 | |
| aggregateToPseudoBulk | 2.495 | 0.065 | 3.136 | |
| aggregateVar | 2.657 | 0.048 | 3.447 | |
| as.dreamletResult | 3.136 | 0.067 | 4.063 | |
| buildClusterTreeFromPB | 1.388 | 0.031 | 1.843 | |
| cellCounts | 2.393 | 0.062 | 3.080 | |
| cellTypeSpecificity | 3.991 | 0.134 | 5.105 | |
| checkFormula | 0.001 | 0.002 | 0.007 | |
| coefNames-methods | 7.549 | 0.086 | 9.355 | |
| compositePosteriorTest | 12.869 | 0.184 | 16.757 | |
| computeCellCounts | 0.290 | 0.021 | 0.383 | |
| computeLogCPM | 0.650 | 0.078 | 0.979 | |
| computeNormCounts | 0.433 | 0.043 | 0.655 | |
| details-methods | 4.357 | 0.079 | 5.539 | |
| diffVar-methods | 10.582 | 0.119 | 13.250 | |
| dreamlet | 8.848 | 0.106 | 11.173 | |
| dreamletCompareClusters | 6.383 | 0.092 | 7.736 | |
| dropRedundantTerms | 0.011 | 0.001 | 0.016 | |
| equalFormulas | 0.001 | 0.001 | 0.001 | |
| extractData-methods | 4.600 | 0.058 | 5.740 | |
| fitVarPart | 48.265 | 0.445 | 61.203 | |
| getExprGeneNames | 6.640 | 0.091 | 8.184 | |
| getTreat-methods | 7.643 | 0.073 | 9.498 | |
| meta_analysis | 36.960 | 0.567 | 47.060 | |
| outlier | 0.006 | 0.001 | 0.010 | |
| outlierByAssay | 4.534 | 0.050 | 5.630 | |
| pbWeights | 6.653 | 0.105 | 8.581 | |
| plotBeeswarm | 9.553 | 0.115 | 11.920 | |
| plotCellComposition | 2.331 | 0.053 | 2.921 | |
| plotForest-methods | 8.108 | 0.071 | 9.932 | |
| plotGeneHeatmap-methods | 9.352 | 0.102 | 11.466 | |
| plotHeatmap-methods | 1.751 | 0.024 | 2.064 | |
| plotPCA | 8.896 | 0.086 | 10.962 | |
| plotPercentBars-methods | 45.596 | 0.331 | 56.200 | |
| plotProjection | 2.277 | 0.075 | 2.852 | |
| plotVarPart-methods | 46.354 | 0.390 | 56.939 | |
| plotViolin-methods | 2.344 | 0.032 | 2.881 | |
| plotVolcano-methods | 10.365 | 0.133 | 12.664 | |
| plotVoom-methods | 6.503 | 0.075 | 7.847 | |
| processAssays | 7.553 | 0.068 | 9.109 | |
| removeConstantTerms | 0.010 | 0.001 | 0.015 | |
| residuals-methods | 7.673 | 0.084 | 9.301 | |
| run_mash | 14.689 | 0.214 | 17.550 | |
| seeErrors-methods | 7.550 | 0.096 | 9.316 | |
| sortCols-method | 46.111 | 0.381 | 56.452 | |
| stackAssays | 25.958 | 0.227 | 31.694 | |
| topTable-methods | 7.597 | 0.063 | 9.008 | |
| zenith_gsa-methods | 178.449 | 9.649 | 228.207 | |