| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:41 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
To the developers/maintainers of the SingleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1903/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SingleR 2.3.0 (landing page) Aaron Lun
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: SingleR |
| Version: 2.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SingleR_2.3.0.tar.gz |
| StartedAt: 2023-05-10 05:05:54 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 05:14:09 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 495.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleR.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SingleR_2.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SingleR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘2.3.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SingleR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 16.5Mb
sub-directories of 1Mb or more:
libs 16.0Mb
* 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 R 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 ... OK
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/SingleR/libs/SingleR.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotScoreDistribution 12.581 0.364 12.945
plotDeltaDistribution 6.871 0.152 7.024
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SingleR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SingleR.Rcheck/00check.log’
for details.
SingleR.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SingleR
###
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##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
105 | virtual std::pair<double, double> dimension_preference () const {
| ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -c integrate_build.cpp -o integrate_build.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
105 | virtual std::pair<double, double> dimension_preference () const {
| ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -c integrate_run.cpp -o integrate_run.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
105 | virtual std::pair<double, double> dimension_preference () const {
| ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -c prebuild.cpp -o prebuild.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
105 | virtual std::pair<double, double> dimension_preference () const {
| ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -c run.cpp -o run.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
105 | virtual std::pair<double, double> dimension_preference () const {
| ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib -o SingleR.so RcppExports.o find_classic_markers.o integrate_build.o integrate_run.o prebuild.o run.o
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-SingleR/00new/SingleR/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 (SingleR)
SingleR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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(SingleR)
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 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, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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
> test_check("SingleR")
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: S4Arrays
Attaching package: 'S4Arrays'
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 5 | SKIP 0 | PASS 294 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 294 ]
>
> proc.time()
user system elapsed
95.445 2.718 156.747
SingleR.Rcheck/SingleR-Ex.timings
| name | user | system | elapsed | |
| SingleR | 1.222 | 0.084 | 1.308 | |
| aggregateReference | 2.500 | 0.036 | 2.537 | |
| classifySingleR | 0.191 | 0.000 | 0.190 | |
| combineCommonResults | 0.519 | 0.012 | 0.531 | |
| combineRecomputedResults | 0.484 | 0.028 | 0.513 | |
| getClassicMarkers | 0.216 | 0.004 | 0.219 | |
| getDeltaFromMedian | 0.319 | 0.012 | 0.331 | |
| matchReferences | 0.521 | 0.004 | 0.526 | |
| mockData | 0.033 | 0.000 | 0.034 | |
| plotDeltaDistribution | 6.871 | 0.152 | 7.024 | |
| plotScoreDistribution | 12.581 | 0.364 | 12.945 | |
| plotScoreHeatmap | 3.425 | 0.036 | 3.463 | |
| pruneScores | 0.392 | 0.012 | 0.404 | |
| rebuildIndex | 0.105 | 0.000 | 0.105 | |
| trainSingleR | 1.584 | 0.024 | 1.609 | |