Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scTGIF.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scTGIF_1.24.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scTGIF.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 ‘scTGIF/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘scTGIF’ version ‘1.24.0’* checking package namespace information ... OK* checking package dependencies ... OK* 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 ‘scTGIF’ can be installed ... OK* 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 ... NOTEUnexported object imported by a ':::' call: ‘schex:::.make_hexbin_function’  See the note in ?`:::` about the use of this operator.* 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 files in ‘vignettes’ ... OK* checking examples ... OK* 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/scTGIF.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scTGIF###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘scTGIF’ ...** this is package ‘scTGIF’ version ‘1.24.0’** using staged installation** R** data** inst** 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 (scTGIF)

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.> library("testthat")> library("scTGIF")> > options(testthat.use_colours = FALSE)> > test_file("testthat/test_DistalLungEpithelium.R")══ Testing test_DistalLungEpithelium.R ═════════════════════════════════════════[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] Done!> test_file("testthat/test_TGIFFunctions.R")══ Testing test_TGIFFunctions.R ════════════════════════════════════════════════[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] Done!> test_file("testthat/test_convertRowID.R")══ Testing test_convertRowID.R ═════════════════════════════════════════════════[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]  |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              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|                                                                              |========================================================              |  80%  |                                                                              |======================================================================| 100%[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ][ FAIL 3 | WARN 0 | SKIP 0 | PASS 5 ]── Failure ('test_convertRowID.R:48:1'): (code run outside of `test_that()`) ───Expected `identical(rownames(out$output), c("3", "2", "4", "7"))` to be TRUE.Differences:`actual`:   FALSE`expected`: TRUE ── Failure ('test_convertRowID.R:51:1'): (code run outside of `test_that()`) ───Expected `identical(rownames(out$output), c("3", "2", "4", "7"))` to be TRUE.Differences:`actual`:   FALSE`expected`: TRUE ── Error ('test_convertRowID.R:53:1'): (code run outside of `test_that()`) ─────Error in `i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value, "value"), check = FALSE)`: Length of new attribute value must be 1 or 5, the number of targetedges, not 4.Backtrace:    ▆ 1. └─scTGIF::convertRowID(input, rowID, LtoR, "large.mean") at test_convertRowID.R:53:1 2.   └─scTGIF (local) f(input, rowID, LtoR, score, unique.right) 3.     └─igraph::`E<-`(`*tmp*`, value = `*vtmp*`) 4.       └─igraph:::i_set_edge_attr(...) 5.         └─cli::cli_abort("Length of new attribute value must be {if (length(index) != 1) '1 or '}{length(index)}, the number of target edges, not {length(value)}.") 6.           └─rlang::abort(...)[ FAIL 3 | WARN 0 | SKIP 0 | PASS 5 ]> test_file("testthat/test_cellMarkerToGmt.R")══ Testing test_cellMarkerToGmt.R ══════════════════════════════════════════════[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 2 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 3 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 1 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 2 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 3 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 4 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 5 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 6 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 7 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 8 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 9 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 10 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 11 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 13 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ][ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]── Warning ('test_cellMarkerToGmt.R:134:1'): (code run outside of `test_that()`) ──1 record(s) contain duplicate ids: MeniscusBacktrace:    ▆ 1. └─GSEABase::getGmt(outfile2_1) at test_cellMarkerToGmt.R:134:1 2.   └─GSEABase:::.warningf(...)── Warning ('test_cellMarkerToGmt.R:135:1'): (code run outside of `test_that()`) ──1 record(s) contain duplicate ids: MeniscusBacktrace:    ▆ 1. └─GSEABase::getGmt(outfile2_2) at test_cellMarkerToGmt.R:135:1 2.   └─GSEABase:::.warningf(...)── Warning ('test_cellMarkerToGmt.R:140:1'): (code run outside of `test_that()`) ──1 record(s) contain duplicate ids: PancreasBacktrace:    ▆ 1. └─GSEABase::getGmt(outfile3_1) at test_cellMarkerToGmt.R:140:1 2.   └─GSEABase:::.warningf(...)── Warning ('test_cellMarkerToGmt.R:141:1'): (code run outside of `test_that()`) ──1 record(s) contain duplicate ids: PancreasBacktrace:    ▆ 1. └─GSEABase::getGmt(outfile3_2) at test_cellMarkerToGmt.R:141:1 2.   └─GSEABase:::.warningf(...)[ FAIL 0 | WARN 4 | SKIP 0 | PASS 16 ]> > proc.time()   user  system elapsed  13.581   0.949  14.528