Shuangbin Xu
| Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 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 2025-09-15 12:03 -0400 (Mon, 15 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4719 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4538 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4522 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4543 |
| 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 2130/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVP 1.1.0 (landing page) Shuangbin Xu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVP.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVP_1.1.0.tar.gz |
| StartedAt: 2025-09-15 04:35:55 -0400 (Mon, 15 Sep 2025) |
| EndedAt: 2025-09-15 04:42:14 -0400 (Mon, 15 Sep 2025) |
| EllapsedTime: 378.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVP.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVP_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVP.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 25.6Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 1.6Mb
libs 22.4Mb
* 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:
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 19.246 0.624 1.135
runSGSA-method 12.960 0.772 12.562
runWKDE-method 7.118 0.191 2.541
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/SVP.Rcheck/00check.log’
for details.
SVP.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SVP
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SVP’ ...
** this is package ‘SVP’ version ‘1.1.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c autocorutils.cpp -o autocorutils.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from autocorutils.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c bisp.cpp -o bisp.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from autocorutils.h:1,
from bisp.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c cor.cpp -o cor.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from cor.cpp:2:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c extract.cpp -o extract.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from extract.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c gearysc.cpp -o gearysc.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from autocorutils.h:1,
from gearysc.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c getisord.cpp -o getisord.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from getisord.cpp:2:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c kld.cpp -o kld.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from kld.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c lisa.cpp -o lisa.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from autocorutils.h:1,
from lisa.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c mca.cpp -o mca.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from mca.cpp:4:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c metric.cpp -o metric.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from autocorutils.h:1,
from metric.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c moransi.cpp -o moransi.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from autocorutils.h:1,
from moransi.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c pairknn.cpp -o pairknn.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from pairknn.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/dqrng/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -Wall -Werror=format-security -c rwr.cpp -o rwr.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from rwr.cpp:1:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -fopenmp -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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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")
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 0.029000 seconds
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|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 0.025000 seconds
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 0.049000 seconds
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
elapsed time is 0.903000 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
30.885 1.353 13.490
SVP.Rcheck/SVP-Ex.timings
| name | user | system | elapsed | |
| CellCycle.Hs | 0.002 | 0.000 | 0.002 | |
| LISAResult | 0.538 | 0.010 | 0.469 | |
| LISAsce-method | 0.838 | 0.090 | 0.792 | |
| SVP-accessors | 2.874 | 0.093 | 2.968 | |
| SVPExperiment | 0.368 | 0.008 | 0.377 | |
| as_tbl_df | 3.955 | 0.035 | 3.982 | |
| cal_lisa_f1-method | 0.221 | 0.047 | 0.131 | |
| cluster.assign-method | 0.285 | 0.002 | 0.287 | |
| data_CancerSEA | 0.006 | 0.000 | 0.006 | |
| data_SenMayo | 0.001 | 0.000 | 0.001 | |
| data_hpda_spe_cell_dec | 0.013 | 0.000 | 0.013 | |
| data_sceSubPbmc | 0.136 | 0.003 | 0.139 | |
| extract_weight_adj-method | 0.132 | 0.000 | 0.132 | |
| fast_cor | 0.007 | 0.000 | 0.002 | |
| fscoreDfs | 1.237 | 0.057 | 1.294 | |
| gsvaExps | 0.799 | 0.003 | 0.802 | |
| mob_marker_genes | 0.001 | 0.000 | 0.001 | |
| mob_sce | 0.321 | 0.003 | 0.323 | |
| plot_heatmap_globalbv | 3.854 | 0.285 | 3.548 | |
| pred.cell.signature-method | 3.107 | 0.121 | 3.233 | |
| runCORR-method | 0.109 | 0.022 | 0.108 | |
| runDetectMarker-method | 0.992 | 0.085 | 1.051 | |
| runDetectSVG-method | 0.737 | 0.030 | 0.704 | |
| runENCODE-method | 1.723 | 0.105 | 1.828 | |
| runGLOBALBV-method | 0.837 | 0.107 | 0.331 | |
| runKldSVG-method | 19.246 | 0.624 | 1.135 | |
| runLISA-method | 1.925 | 0.119 | 2.007 | |
| runLOCALBV-method | 0.940 | 0.006 | 0.945 | |
| runMCA-method | 0.812 | 0.033 | 0.826 | |
| runSGSA-method | 12.960 | 0.772 | 12.562 | |
| runWKDE-method | 7.118 | 0.191 | 2.541 | |
| svDfs | 0.465 | 0.011 | 0.477 | |