Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sparrow_1.16.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sparrow.Rcheck’* using R version 4.5.0 (2025-04-11)* using platform: aarch64-unknown-linux-gnu* R was compiled by    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0    GNU Fortran (GCC) 14.2.0* running under: openEuler 24.03 (LTS)* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘sparrow/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘sparrow’ version ‘1.16.0’* package encoding: UTF-8* 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 ‘sparrow’ can be installed ... OK* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... NOTELicense stub is invalid DCF.* 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 whether startup messages can be suppressed ... 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 ... NOTE.map_ids_orthogene: no visible binding for global variable ‘gspecies’.map_ids_orthogene: no visible binding for global variable ‘species’.map_ids_orthogene: no visible binding for global variable ‘input_ensg’.map_ids_orthogene: no visible binding for global variable  ‘ortholog_ensg’.map_ids_orthogene: no visible binding for global variable  ‘ortholog_gene’.map_ids_orthogene: no visible binding for global variable ‘symbol’.map_ids_orthogene: no visible binding for global variable ‘input_id’.map_ids_orthogene: no visible global function definition for  ‘starts_with’.map_ids_orthogene: no visible global function definition for  ‘last_col’.map_ids_orthogene: no visible binding for global variable ‘rm_na’geneSetsStats: no visible binding for global variable ‘direction’getMSigGeneSetDb: no visible binding for global variable ‘ncbi_gene’getMSigGeneSetDb: no visible binding for global variable ‘db_species’getMSigGeneSetDb: no visible binding for global variable  ‘msigdb_collection’getMSigGeneSetDb: no visible binding for global variable ‘gene_symbol’getMSigGeneSetDb: no visible binding for global variable  ‘gs_collection_name’getMSigGeneSetDb: no visible binding for global variable ‘gs_url’convertIdentifiers,GeneSetDb: no visible binding for global variable  ‘.convert_ids_with_babelgene’convertIdentifiers,GeneSetDb: no visible global function definition for  ‘.map_ids_babelgene’Undefined global functions or variables:  .convert_ids_with_babelgene .map_ids_babelgene db_species direction  gene_symbol gs_collection_name gs_url gspecies input_ensg input_id  last_col msigdb_collection ncbi_gene ortholog_ensg ortholog_gene  rm_na species starts_with symbol* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTENon-topic package-anchored link(s) in Rd file 'GeneSetDb-class.Rd':  ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’Non-topic package-anchored link(s) in Rd file 'calculateIndividualLogFC.Rd':  ‘[limma:ebayes]{limma::eBayes()}’Non-topic package-anchored link(s) in Rd file 'collectionMetadata.Rd':  ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’Non-topic package-anchored link(s) in Rd file 'seas.Rd':  ‘[limma:toptable]{limma::topTable()}’  ‘[limma:dupcor]{limma::duplicateCorrelation()}’See section 'Cross-references' in the 'Writing R Extensions' manual.Found the following Rd file(s) with Rd \link{} targets missing packageanchors:  seas.Rd: BiocParallelPlease provide package anchors for all Rd \link{} targets not in thepackage 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 line endings in Makefiles ... OK* checking for GNU extensions in Makefiles ... OK* checking include directives in Makefiles ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                            user system elapsedscoreSingleSamples        14.344  0.171  14.529goseq                     11.140  0.275  11.131seas                       8.051  0.256   8.019geneSetsStats              6.937  0.128   6.477eigenWeightedMean          6.784  0.167   6.948annotateGeneSetMembership  5.940  0.180   5.823SparrowResult-utilities    5.801  0.159   5.665geneSetSummaryByGenes      4.841  0.179   4.696* 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* DONEStatus: 3 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/sparrow.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD INSTALL sparrow###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘sparrow’ ...** this is package ‘sparrow’ version ‘1.16.0’** using staged installation** R** inst** 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** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (sparrow)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-unknown-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("sparrow")> library("testthat")> library("data.table")> library("dplyr")Attaching package: 'dplyr'The following objects are masked from 'package:data.table':    between, first, lastThe following object is masked from 'package:testthat':    matchesThe following object is masked from 'package:sparrow':    combineThe following objects are masked from 'package:stats':    filter, lagThe following objects are masked from 'package:base':    intersect, setdiff, setequal, union> > test_check("sparrow")Attaching package: 'magrittr'The following objects are masked from 'package:testthat':    equals, is_less_than, not[ FAIL 0 | WARN 0 | SKIP 6 | PASS 1463 ]══ Skipped tests (6) ═══════════════════════════════════════════════════════════• empty test (1): 'test-MultiGSEAResult.R:3:1'• {misgdbdf} is not installed (5): 'test-get-msigdb.R:6:3',  'test-get-msigdb.R:14:3', 'test-get-msigdb.R:27:3', 'test-get-msigdb.R:65:3',  'test-get-msigdb.R:99:3'[ FAIL 0 | WARN 0 | SKIP 6 | PASS 1463 ]> > ## Remove temporary files that were generated> test.dir <- system.file('tests', package = "sparrow")> pdfs <- dir(test.dir, "\\.pdf$", full.names=TRUE)> if (length(pdfs)) {+   unlink(pdfs)+ }> > > proc.time()   user  system elapsed 341.580   7.880 330.423