Shuangbin Xu
| Snapshot Date: 2025-06-12 13:25 -0400 (Thu, 12 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/SVP |
| git_branch: devel |
| git_last_commit: a9a165a |
| git_last_commit_date: 2025-04-15 13:49:09 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-13 12:09 -0400 (Fri, 13 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4797 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4538 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4571 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4515 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4483 |
| 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 2112/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVP 1.1.0 (landing page) Shuangbin Xu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the SVP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SVP.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: SVP |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVP_1.1.0.tar.gz |
| StartedAt: 2025-06-13 00:01:52 -0400 (Fri, 13 Jun 2025) |
| EndedAt: 2025-06-13 00:07:08 -0400 (Fri, 13 Jun 2025) |
| EllapsedTime: 315.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVP_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVP.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVP/DESCRIPTION’ ... OK
* this is package ‘SVP’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘SVP’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
LISAResult.Rd: SingleCellExperiment-class
LISAsce-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class
SVPExperiment.Rd: SingleCellExperiment, SingleCellExperiment-class
cal_lisa_f1-method.Rd: SingleCellExperiment-class
cluster.assign-method.Rd: SingleCellExperiment-class
data_hpda_spe_cell_dec.Rd: SpatialExperiment-class
data_sceSubPbmc.Rd: SingleCellExperiment-class
extract_weight_adj-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class
fscoreDfs.Rd: SingleCellExperiment-class, DataFrame-class, List-class
gsvaExps.Rd: SingleCellExperiment-class, colData, List-class,
assay<-, Annotated-class, metadata, Vector-class, mcols
mob_sce.Rd: SingleCellExperiment-class
pred.cell.signature-method.Rd: SingleCellExperiment-class
runCORR-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class
runDetectSVG-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class, SimpleList-class, DataFrame-class
runENCODE-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class
runGLOBALBV-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class
runKldSVG-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class, SimpleList-class, DataFrame-class
runLISA-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class, SimpleList-class
runLOCALBV-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class, SimpleList-class
runMCA-method.Rd: SingleCellExperiment-class
runSGSA-method.Rd: SingleCellExperiment-class
runWKDE-method.Rd: SingleCellExperiment-class,
SpatialExperiment-class
svDfs.Rd: SingleCellExperiment-class, DataFrame-class, List-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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... INFO
GNU make is a SystemRequirements.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runKldSVG-method 14.974 1.898 1.279
runSGSA-method 14.901 0.962 14.931
runWKDE-method 7.351 0.345 3.652
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/SVP.Rcheck/00check.log’
for details.
SVP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘SVP’ ... ** this is package ‘SVP’ version ‘1.1.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c autocorutils.cpp -o autocorutils.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c bisp.cpp -o bisp.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c cor.cpp -o cor.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c extract.cpp -o extract.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c gearysc.cpp -o gearysc.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c getisord.cpp -o getisord.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c kld.cpp -o kld.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c lisa.cpp -o lisa.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c mca.cpp -o mca.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c metric.cpp -o metric.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c moransi.cpp -o moransi.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c pairknn.cpp -o pairknn.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/dqrng/include' -I/opt/R/x86_64/include -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fPIC -falign-functions=64 -Wall -g -O2 -c rwr.cpp -o rwr.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SVP.so RcppExports.o autocorutils.o bisp.o cor.o extract.o gearysc.o getisord.o kld.o lisa.o mca.o metric.o moransi.o pairknn.o rwr.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-SVP/00new/SVP/libs ** R ** data ** 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 (SVP)
SVP.Rcheck/tests/testthat.Rout
R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(SVP)
>
> test_check("SVP")
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elapsed time is 0.036000 seconds
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elapsed time is 0.095000 seconds
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elapsed time is 0.029000 seconds
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elapsed time is 0.961000 seconds
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
The result is added to the input object, which can be extracted using
`LISAResult()` with `type='localG.SVP'`, and a specified `features`.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
>
> proc.time()
user system elapsed
28.775 4.252 15.813
SVP.Rcheck/SVP-Ex.timings
| name | user | system | elapsed | |
| CellCycle.Hs | 0.002 | 0.002 | 0.004 | |
| LISAResult | 0.535 | 0.025 | 0.568 | |
| LISAsce-method | 0.935 | 0.238 | 0.994 | |
| SVP-accessors | 3.846 | 0.134 | 4.010 | |
| SVPExperiment | 0.580 | 0.024 | 0.608 | |
| as_tbl_df | 3.411 | 0.164 | 3.499 | |
| cal_lisa_f1-method | 0.189 | 0.365 | 0.168 | |
| cluster.assign-method | 0.416 | 0.198 | 0.438 | |
| data_CancerSEA | 0.023 | 0.005 | 0.027 | |
| data_SenMayo | 0.001 | 0.001 | 0.002 | |
| data_hpda_spe_cell_dec | 0.013 | 0.002 | 0.015 | |
| data_sceSubPbmc | 0.263 | 0.007 | 0.273 | |
| extract_weight_adj-method | 0.158 | 0.003 | 0.162 | |
| fast_cor | 0.004 | 0.004 | 0.003 | |
| fscoreDfs | 1.446 | 0.205 | 1.482 | |
| gsvaExps | 1.153 | 0.034 | 1.199 | |
| mob_marker_genes | 0.001 | 0.001 | 0.002 | |
| mob_sce | 0.567 | 0.012 | 0.583 | |
| plot_heatmap_globalbv | 2.826 | 0.704 | 2.315 | |
| pred.cell.signature-method | 4.496 | 0.340 | 4.878 | |
| runCORR-method | 0.119 | 0.020 | 0.127 | |
| runDetectMarker-method | 1.212 | 0.547 | 1.262 | |
| runDetectSVG-method | 0.877 | 0.687 | 0.844 | |
| runENCODE-method | 1.104 | 0.050 | 1.160 | |
| runGLOBALBV-method | 0.886 | 0.310 | 0.364 | |
| runKldSVG-method | 14.974 | 1.898 | 1.279 | |
| runLISA-method | 2.116 | 0.436 | 2.159 | |
| runLOCALBV-method | 0.990 | 0.018 | 1.012 | |
| runMCA-method | 0.971 | 0.035 | 1.011 | |
| runSGSA-method | 14.901 | 0.962 | 14.931 | |
| runWKDE-method | 7.351 | 0.345 | 3.652 | |
| svDfs | 0.599 | 0.022 | 0.623 | |