Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scider_1.8.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scider.Rcheck’* using R version 4.5.2 (2025-10-31)* 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 ‘scider/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘scider’ version ‘1.8.0’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... INFOImports includes 23 non-default packages.Importing from so many packages makes the package vulnerable to any ofthem becoming unavailable.  Move as many as possible to Suggests anduse 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 ‘scider’ can be installed ... OK* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’* 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 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 ... OK* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking 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 compiled code ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                user system elapsedplotDR        43.233  0.221  25.460runUMAP       30.041  0.171  25.233getClusters   15.100  0.517  14.042findNbrsSNN   10.320  0.338   9.123runPCA         6.628  0.135   6.763localMoran     5.707  0.010   1.585allocateCells  4.962  0.377   5.345* 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* DONEStatus: 1 NOTESee  ‘/home/biocbuild/bbs-3.22-bioc/meat/scider.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scider###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘scider’ ...** this is package ‘scider’ version ‘1.8.0’** using staged installation** libsusing 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/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c C_findSNN.cpp -o C_findSNN.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c C_globalMoran.cpp -o C_globalMoran.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c C_localMoran.cpp -o C_localMoran.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.og++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o scider.so C_findSNN.o C_globalMoran.o C_localMoran.o utils.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-scider/00new/scider/libs** R** data** byte-compile and prepare package for lazy loading** help*** installing help indices*** copying figures** 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 (scider)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> # 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(scider)> > test_check("scider")Assigning cells to ROIs defined by Breast cancer No contour detected. Proceed without contour.Using bins = 10 to draw contours with equal cell numbers.Assigning cells to ROIs defined by Breast cancer Assigning cells to contour levels of Breast cancer Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUEUsing bins = 10 to draw contours with equal cell numbers.cell_typess is not a column of the colData. Skipping cell_typessUsing bins = 10 to draw contours with equal cell numbers.Assigning cells to ROIs defined by Breast cancer fibroblasts Assigning cells to contour levels of Breast cancer Using bins = 10 to draw contours with equal cell numbers.Assigning cells to ROIs defined by Breast cancer No contour detected. Proceed without contour.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 71 ]> > proc.time()   user  system elapsed  33.504   1.257  34.756