Shuangbin Xu
| Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 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 2025-08-04 11:45 -0400 (Mon, 04 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: /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_1.0.2.tar.gz |
| StartedAt: 2025-08-01 11:01:52 -0400 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 11:11:34 -0400 (Fri, 01 Aug 2025) |
| EllapsedTime: 581.9 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_1.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SVP.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.0.2’
* 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 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
runSGSA-method 21.526 0.569 21.986
runKldSVG-method 20.191 1.697 2.582
runWKDE-method 10.483 0.246 5.582
pred.cell.signature-method 8.699 0.458 9.310
SVP-accessors 6.627 0.229 7.231
as_tbl_df 6.563 0.080 6.776
plot_heatmap_globalbv 5.831 0.087 5.077
* 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-3.21-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 ‘1.0.2’ ** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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 0.061000 seconds
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elapsed time is 0.137000 seconds
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elapsed time is 0.049000 seconds
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 1.973000 seconds
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
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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
46.698 2.962 31.004
SVP.Rcheck/SVP-Ex.timings
| name | user | system | elapsed | |
| CellCycle.Hs | 0.003 | 0.003 | 0.010 | |
| LISAResult | 1.057 | 0.058 | 1.135 | |
| LISAsce-method | 1.850 | 0.148 | 1.985 | |
| SVP-accessors | 6.627 | 0.229 | 7.231 | |
| SVPExperiment | 0.895 | 0.026 | 0.926 | |
| as_tbl_df | 6.563 | 0.080 | 6.776 | |
| cal_lisa_f1-method | 0.311 | 0.019 | 0.306 | |
| cluster.assign-method | 0.721 | 0.042 | 0.777 | |
| data_CancerSEA | 0.012 | 0.007 | 0.020 | |
| data_SenMayo | 0.002 | 0.003 | 0.005 | |
| data_hpda_spe_cell_dec | 0.024 | 0.004 | 0.029 | |
| data_sceSubPbmc | 0.391 | 0.009 | 0.413 | |
| extract_weight_adj-method | 0.305 | 0.006 | 0.312 | |
| fast_cor | 0.003 | 0.001 | 0.004 | |
| fscoreDfs | 2.744 | 0.058 | 2.808 | |
| gsvaExps | 2.117 | 0.042 | 2.334 | |
| mob_marker_genes | 0.002 | 0.003 | 0.005 | |
| mob_sce | 0.789 | 0.019 | 0.840 | |
| plot_heatmap_globalbv | 5.831 | 0.087 | 5.077 | |
| pred.cell.signature-method | 8.699 | 0.458 | 9.310 | |
| runCORR-method | 0.200 | 0.023 | 0.225 | |
| runDetectMarker-method | 2.010 | 0.104 | 2.109 | |
| runDetectSVG-method | 1.748 | 0.097 | 1.748 | |
| runENCODE-method | 2.200 | 0.122 | 2.330 | |
| runGLOBALBV-method | 1.512 | 0.044 | 0.759 | |
| runKldSVG-method | 20.191 | 1.697 | 2.582 | |
| runLISA-method | 3.988 | 0.098 | 4.073 | |
| runLOCALBV-method | 1.912 | 0.027 | 1.973 | |
| runMCA-method | 1.693 | 0.045 | 1.743 | |
| runSGSA-method | 21.526 | 0.569 | 21.986 | |
| runWKDE-method | 10.483 | 0.246 | 5.582 | |
| svDfs | 1.114 | 0.032 | 1.152 | |