Aaron Lun
| Snapshot Date: 2024-12-08 13:40 -0500 (Sun, 08 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/scran |
| git_branch: devel |
| git_last_commit: f18e781 |
| git_last_commit_date: 2024-10-29 10:09:52 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-09 11:47 -0500 (Mon, 09 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4749 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4461 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4411 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4366 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4241 |
| 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 1880/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scran 1.35.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the scran package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/scran.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: scran |
| Version: 1.35.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scran_1.35.0.tar.gz |
| StartedAt: 2024-12-09 09:48:02 -0000 (Mon, 09 Dec 2024) |
| EndedAt: 2024-12-09 10:03:08 -0000 (Mon, 09 Dec 2024) |
| EllapsedTime: 906.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scran.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scran_1.35.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (conda-forge gcc 14.2.0-1) 14.2.0
GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.35.0’
* 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 ‘scran’ can be installed ... OK
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 9.1Mb
sub-directories of 1Mb or more:
libs 8.0Mb
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
buildSNNGraph.Rd: SingleCellExperiment-class, makeSNNGraph,
makeKNNGraph, SummarizedExperiment-class, reducedDims,
BiocSingularParam-class, BiocParallelParam-class, graph,
cluster_walktrap
clusterCells.Rd: SingleCellExperiment-class, clusterRows,
SummarizedExperiment-class, BlusterParam-class
combineBlocks.Rd: DataFrame-class, combineParallelPValues
combineMarkers.Rd: DataFrame-class, BiocParallelParam-class,
List-class, combineParallelPValues
combinePValues.Rd: combineParallelPValues
combineVar.Rd: DataFrame-class, combineParallelPValues
computeSumFactors.Rd: pooledSizeFactors, computePooledFactors,
sizeFactors
convertTo.Rd: SingleCellExperiment-class
correlateGenes.Rd: DataFrame-class
correlateNull.Rd: BiocParallelParam-class
correlatePairs.Rd: SummarizedExperiment-class,
BiocParallelParam-class, DataFrame-class, parallelStouffer
cyclone.Rd: SummarizedExperiment-class, BiocParallelParam-class
decideTestsPerLabel.Rd: decideTests, List-class
defunct.Rd: bootstrapStability, pairwiseModularity, neighborPurity,
clusterRows, NNGraphParam-class, TwoStepParam-class, pairwiseRand
denoisePCA.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, DataFrame-class,
BiocSingularParam-class, BiocParallelParam-class, reducedDimNames,
assays, reducedDims, LowRankMatrix-class, runSVD
findMarkers.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, colLabels, DataFrame-class,
BiocParallelParam-class
fitTrendPoisson.Rd: BiocParallelParam-class
fitTrendVar.Rd: weightedLowess
fixedPCA.Rd: SingleCellExperiment-class, reducedDimNames, assays,
BiocSingularParam-class, BiocParallelParam-class, reducedDims,
LowRankMatrix-class
gene_selection.Rd: Rle-class, SingleCellExperiment-class,
calculateAverage
getClusteredPCs.Rd: clusterRows, BlusterParam-class, makeSNNGraph,
cluster_walktrap, DataFrame-class, List-class, runPCA
getMarkerEffects.Rd: DataFrame-class
getTopHVGs.Rd: DataFrame-class, SummarizedExperiment-class
getTopMarkers.Rd: DataFrame-class, List-class
modelGeneCV2.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, combineParallelPValues,
BiocParallelParam-class, librarySizeFactors, sizeFactors,
DataFrame-class
modelGeneCV2WithSpikes.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, altExp, combineParallelPValues,
BiocParallelParam-class, DataFrame-class, librarySizeFactors,
sizeFactors
modelGeneVar.Rd: SummarizedExperiment-class, combineParallelPValues,
BiocParallelParam-class, DataFrame-class
modelGeneVarByPoisson.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, combineParallelPValues,
BiocParallelParam-class, librarySizeFactors, sizeFactors,
DataFrame-class
modelGeneVarWithSpikes.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, altExp, combineParallelPValues,
BiocParallelParam-class, DataFrame-class, librarySizeFactors,
sizeFactors
multiMarkerStats.Rd: DataFrame-class, List-class
pairwiseBinom.Rd: colLabels, BiocParallelParam-class,
DataFrame-class, binomTest
pairwiseTTests.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, colLabels, BiocParallelParam-class,
DataFrame-class, logNormCounts
pairwiseWilcox.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, colLabels, BiocParallelParam-class,
DataFrame-class
pseudoBulkDGE.Rd: DataFrame-class, makeContrasts, glmTreat, treat,
voomWithQualityWeights, sumCountsAcrossCells, voom, List-class,
topTags, topTable, metadata, filterByExpr
pseudoBulkSpecific.Rd: treat, List-class, DataFrame-class
quickCluster.Rd: SummarizedExperiment-class, NNGraphParam,
HclustParam, BiocSingularParam-class, BiocParallelParam-class,
dgCMatrix-class, calculateAverage
quickSubCluster.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, BlusterParam-class, clusterRows,
reducedDims, List-class, metadata
sandbag.Rd: SummarizedExperiment-class
scaledColRanks.Rd: BiocParallelParam-class
scoreMarkers.Rd: SummarizedExperiment-class, BiocParallelParam-class,
correctGroupSummary
summaryMarkerStats.Rd: SummarizedExperiment-class,
SingleCellExperiment-class, colLabels, DataFrame-class,
sumCountsAcrossCells, BiocParallelParam-class, List-class
testLinearModel.Rd: SummarizedExperiment-class,
combineParallelPValues, BiocParallelParam-class, lmFit,
fitLinearModel, DataFrame-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning in combinePValues(p1, p2, p3) : 'combinePValues' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cyclone 31.073 0.116 31.254
buildSNNGraph 6.644 0.072 5.327
pseudoBulkSpecific 6.407 0.168 6.587
quickSubCluster 4.966 0.044 4.299
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck/00check.log’
for details.
scran.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL scran ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘scran’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c choose_effect_size.cpp -o choose_effect_size.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c combine_rho.cpp -o combine_rho.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c compute_blocked_stats.cpp -o compute_blocked_stats.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c compute_residual_stats.cpp -o compute_residual_stats.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c compute_rho_null.cpp -o compute_rho_null.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c cyclone_scores.cpp -o cyclone_scores.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c overlap_exprs.cpp -o overlap_exprs.o g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c rand_custom.cpp -o rand_custom.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o -lopenblas -L -L -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-scran/00new/scran/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (scran)
scran.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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(testthat)
> library(scran)
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
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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
Loading required package: scuttle
> test_check("scran")
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
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
[ FAIL 0 | WARN 192 | SKIP 1 | PASS 4479 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• monocle is a little broken because of clusterApply (1): 'test-convert.R:71:5'
[ FAIL 0 | WARN 192 | SKIP 1 | PASS 4479 ]
>
> proc.time()
user system elapsed
478.762 15.885 561.583
scran.Rcheck/scran-Ex.timings
| name | user | system | elapsed | |
| DM | 0.066 | 0.004 | 0.070 | |
| buildSNNGraph | 6.644 | 0.072 | 5.327 | |
| clusterCells | 1.561 | 0.024 | 1.432 | |
| combineBlocks | 1.039 | 0.020 | 1.061 | |
| combineMarkers | 1.788 | 0.040 | 1.833 | |
| combinePValues | 0.042 | 0.000 | 0.042 | |
| combineVar | 1.862 | 0.036 | 1.902 | |
| computeMinRank | 0.002 | 0.000 | 0.002 | |
| convertTo | 1.365 | 0.072 | 1.441 | |
| correlateGenes | 0.813 | 0.007 | 0.823 | |
| correlateNull | 0.320 | 0.000 | 0.321 | |
| correlatePairs | 1.734 | 0.083 | 1.821 | |
| cyclone | 31.073 | 0.116 | 31.254 | |
| decideTestsPerLabel | 4.479 | 0.088 | 4.627 | |
| defunct | 0.000 | 0.001 | 0.001 | |
| denoisePCA | 1.407 | 0.022 | 1.035 | |
| findMarkers | 2.603 | 0.028 | 2.599 | |
| fitTrendCV2 | 0.905 | 0.036 | 0.943 | |
| fitTrendPoisson | 0.235 | 0.008 | 0.244 | |
| fitTrendVar | 0.692 | 0.024 | 0.717 | |
| fixedPCA | 1.134 | 0.040 | 0.944 | |
| getClusteredPCs | 3.719 | 0.087 | 3.660 | |
| getMarkerEffects | 1.109 | 0.048 | 1.163 | |
| getTopHVGs | 0.876 | 0.024 | 0.902 | |
| getTopMarkers | 1.877 | 0.084 | 1.964 | |
| logBH | 0.001 | 0.000 | 0.001 | |
| modelGeneCV2 | 1.098 | 0.020 | 1.120 | |
| modelGeneCV2WithSpikes | 1.030 | 0.028 | 1.060 | |
| modelGeneVar | 1.255 | 0.028 | 1.286 | |
| modelGeneVarByPoisson | 1.039 | 0.032 | 1.073 | |
| modelGeneVarWithSpikes | 1.105 | 0.048 | 1.155 | |
| multiMarkerStats | 1.791 | 0.036 | 1.831 | |
| pairwiseBinom | 0.881 | 0.024 | 0.907 | |
| pairwiseTTests | 0.954 | 0.008 | 0.964 | |
| pairwiseWilcox | 0.792 | 0.024 | 0.817 | |
| pseudoBulkDGE | 3.550 | 0.051 | 3.608 | |
| pseudoBulkSpecific | 6.407 | 0.168 | 6.587 | |
| quickCluster | 2.212 | 0.008 | 1.589 | |
| quickSubCluster | 4.966 | 0.044 | 4.299 | |
| rhoToPValue | 0 | 0 | 0 | |
| sandbag | 0.846 | 0.012 | 0.842 | |
| scaledColRanks | 1.541 | 0.000 | 1.223 | |
| scoreMarkers | 1.259 | 0.028 | 1.289 | |
| summaryMarkerStats | 0.840 | 0.020 | 0.861 | |
| testLinearModel | 0.074 | 0.000 | 0.075 | |