Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings diffcyt_1.30.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/diffcyt.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 ‘diffcyt/DESCRIPTION’ ... OK* this is package ‘diffcyt’ version ‘1.30.0’* 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 ‘diffcyt’ 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 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 ... NOTEcalcCounts: no visible binding for global variable ‘cluster_id’calcCounts: no visible binding for global variable ‘sample_id’calcMedians: no visible binding for global variable ‘cluster_id’calcMedians: no visible binding for global variable ‘sample_id’calcMedians: no visible binding for global variable ‘value’calcMediansByClusterMarker: no visible binding for global variable  ‘cluster_id’calcMediansByClusterMarker: no visible binding for global variable  ‘marker_id’calcMediansByClusterMarker: no visible binding for global variable  ‘value’calcMediansBySampleMarker: no visible binding for global variable  ‘sample_id’calcMediansBySampleMarker: no visible binding for global variable  ‘marker_id’calcMediansBySampleMarker: no visible binding for global variable  ‘value’Undefined global functions or variables:  cluster_id marker_id sample_id value* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  calcCounts.Rd: SummarizedExperiment  calcMedians.Rd: SummarizedExperiment  calcMediansByClusterMarker.Rd: SummarizedExperiment  calcMediansBySampleMarker.Rd: SummarizedExperiment  diffcyt.Rd: flowSet, flowFrame, DataFrame, tbl_df, estimateDisp,    duplicateCorrelation, eBayes  generateClusters.Rd: BuildSOM, SummarizedExperiment, FlowSOM,    BuildMST, rowData  prepareData.Rd: flowSet, flowFrame, DataFrame, tbl_df,    SummarizedExperiment  testDA_GLMM.Rd: SummarizedExperiment, rowData  testDA_edgeR.Rd: SummarizedExperiment, estimateDisp, edgeR, rowData  testDA_voom.Rd: SummarizedExperiment, duplicateCorrelation, voom,    limma, rowData  testDS_LMM.Rd: SummarizedExperiment, rowData  testDS_limma.Rd: SummarizedExperiment, duplicateCorrelation, eBayes,    limma, rowData  topTable.Rd: SummarizedExperiment, DataFrame  transformData.Rd: SummarizedExperimentPlease 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 files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s             user system elapseddiffcyt     9.080  0.110   9.190testDA_GLMM 7.005  0.031   7.036plotHeatmap 5.941  0.112   6.053* 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: 3 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/diffcyt.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL diffcyt###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘diffcyt’ ...** this is package ‘diffcyt’ version ‘1.30.0’** using staged installation** R** 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 (diffcyt)

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(diffcyt)> > test_check("diffcyt")[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]> > proc.time()   user  system elapsed   9.993   0.579  10.562