Shuangbin Xu
| Snapshot Date: 2025-08-07 13:40 -0400 (Thu, 07 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/SVP |
| git_branch: RELEASE_3_21 |
| git_last_commit: 951bd75 |
| git_last_commit_date: 2025-06-15 05:11:04 -0400 (Sun, 15 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-11 11:43 -0400 (Mon, 11 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 2140/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVP 1.0.2 (landing page) Shuangbin Xu
| nebbiolo1 | Linux (Ubuntu 24.04.2 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 | | ||||||||
| kunpeng2 | 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: 1.0.2 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SVP.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SVP_1.0.2.tar.gz |
| StartedAt: 2025-08-08 07:15:34 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 07:21:49 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 375.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SVP.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SVP_1.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SVP.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SVP/DESCRIPTION' ... OK
* this is package 'SVP' version '1.0.2'
* 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 whether package 'SVP' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking installed package size ... INFO
installed size is 5.0Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 1.6Mb
libs 1.9Mb
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/SVP/libs/x64/SVP.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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
runKldSVG-method 22.29 0.31 2.38
runSGSA-method 19.19 0.71 20.64
runWKDE-method 5.78 0.42 2.52
pred.cell.signature-method 4.62 0.47 5.68
* 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
'E:/biocbuild/bbs-3.21-bioc/meat/SVP.Rcheck/00check.log'
for details.
SVP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SVP ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'SVP' ... ** this is package 'SVP' version '1.0.2' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c autocorutils.cpp -o autocorutils.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bisp.cpp -o bisp.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cor.cpp -o cor.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extract.cpp -o extract.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gearysc.cpp -o gearysc.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getisord.cpp -o getisord.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kld.cpp -o kld.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lisa.cpp -o lisa.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mca.cpp -o mca.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c metric.cpp -o metric.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c moransi.cpp -o moransi.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairknn.cpp -o pairknn.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/dqrng/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rwr.cpp -o rwr.o g++ -std=gnu++17 -shared -s -static-libgcc -o SVP.dll tmp.def 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 -fopenmp -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LE:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/libs/x64 -lRcppParallel -LE:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-SVP/00new/SVP/libs/x64 ** 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 ** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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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 0.030000 seconds
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 0.020000 seconds
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 0.040000 seconds
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 1.930000 seconds
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
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
37.51 2.50 18.43
SVP.Rcheck/SVP-Ex.timings
| name | user | system | elapsed | |
| CellCycle.Hs | 0.00 | 0.01 | 0.02 | |
| LISAResult | 0.63 | 0.05 | 0.65 | |
| LISAsce-method | 1.10 | 0.06 | 1.17 | |
| SVP-accessors | 3.19 | 0.24 | 4.49 | |
| SVPExperiment | 1.52 | 0.01 | 1.53 | |
| as_tbl_df | 4.08 | 0.14 | 4.33 | |
| cal_lisa_f1-method | 0.24 | 0.05 | 0.23 | |
| cluster.assign-method | 0.32 | 0.06 | 0.40 | |
| data_CancerSEA | 0.02 | 0.02 | 0.03 | |
| data_SenMayo | 0 | 0 | 0 | |
| data_hpda_spe_cell_dec | 0.03 | 0.02 | 0.05 | |
| data_sceSubPbmc | 0.16 | 0.02 | 0.17 | |
| extract_weight_adj-method | 0.22 | 0.03 | 0.25 | |
| fast_cor | 0.01 | 0.01 | 0.03 | |
| fscoreDfs | 1.52 | 0.10 | 1.63 | |
| gsvaExps | 1.01 | 0.03 | 1.05 | |
| mob_marker_genes | 0 | 0 | 0 | |
| mob_sce | 0.44 | 0.01 | 0.45 | |
| plot_heatmap_globalbv | 3.24 | 0.11 | 2.72 | |
| pred.cell.signature-method | 4.62 | 0.47 | 5.68 | |
| runCORR-method | 0.14 | 0.02 | 0.16 | |
| runDetectMarker-method | 2.61 | 0.06 | 2.63 | |
| runDetectSVG-method | 1.24 | 0.14 | 1.35 | |
| runENCODE-method | 1.31 | 0.00 | 1.31 | |
| runGLOBALBV-method | 1.04 | 0.08 | 0.45 | |
| runKldSVG-method | 22.29 | 0.31 | 2.38 | |
| runLISA-method | 2.39 | 0.25 | 2.67 | |
| runLOCALBV-method | 1.11 | 0.03 | 1.14 | |
| runMCA-method | 1.17 | 0.06 | 1.23 | |
| runSGSA-method | 19.19 | 0.71 | 20.64 | |
| runWKDE-method | 5.78 | 0.42 | 2.52 | |
| svDfs | 0.86 | 0.00 | 0.97 | |