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################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BUSseq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BUSseq_1.16.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BUSseq.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 ‘BUSseq/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘BUSseq’ version ‘1.16.0’* 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 ‘BUSseq’ 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 LazyData ... 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 ... OK* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK* checking use of PKG_*FLAGS in Makefiles ... OK* checking compiled code ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OK* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘BUSseq_example.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/BUSseq.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BUSseq###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘BUSseq’ ...** this is package ‘BUSseq’ version ‘1.16.0’** using staged installation** libsusing C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’/home/biocbuild/bbs-3.22-bioc/R/share/make/shlib.mk:10: warning: overriding recipe for target 'BUSseq.so'Makevars:9: warning: ignoring old recipe for target 'BUSseq.so'g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c BUSseq.cpp -o BUSseq.oBUSseq.cpp: In function ‘double postprob_DE_thr_fun(double*, double, int, int)’:BUSseq.cpp:964:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]  964 |     while((fdr <= _fdr_threshold) & (kappa <= postprob_DE_thr) & (i < (unsigned)vec_PPI.size())){      |                                                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~BUSseq.cpp: In function ‘void BUSseq_inference(int*, int*, int*, int*, char**, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, double*)’:BUSseq.cpp:2674:14: warning: variable ‘All_Drop’ set but not used [-Wunused-but-set-variable] 2674 |         bool All_Drop = true;      |              ^~~~~~~~g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rngstream.cpp -o rngstream.og++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o BUSseq.so BUSseq.o rngstream.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 -lRinstalling to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-BUSseq/00new/BUSseq/libs** R** data*** moving datasets to lazyload DB** 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** 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 (BUSseq)

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.> #######################################> # Apply BUSseq to the Simulation Data #> #######################################> library(BUSseq)> library(SingleCellExperiment)Loading required package: SummarizedExperimentLoading required package: MatrixGenericsLoading required package: matrixStatsAttaching package: 'MatrixGenerics'The following objects are masked from 'package:matrixStats':    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,    colWeightedMeans, colWeightedMedians, colWeightedSds,    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,    rowWeightedSds, rowWeightedVarsLoading required package: GenomicRangesLoading required package: stats4Loading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,    as.data.frame, basename, cbind, colnames, dirname, do.call,    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minLoading required package: S4VectorsAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading required package: IRangesLoading required package: SeqinfoLoading required package: BiobaseWelcome to Bioconductor    Vignettes contain introductory material; view with    'browseVignettes()'. To cite Bioconductor, see    'citation("Biobase")', and for packages 'citation("pkgname")'.Attaching package: 'Biobase'The following object is masked from 'package:MatrixGenerics':    rowMediansThe following objects are masked from 'package:matrixStats':    anyMissing, rowMedians> RawCountData <- assay(BUSseqfits_example, "counts")> batch_ind <- unlist(colData(BUSseqfits_example))> sce <- SingleCellExperiment(assays = list(counts = RawCountData),+                             colData = DataFrame(Batch_ind = batch_ind))> BUSseqfits_res <- BUSseq_MCMC(ObservedData = sce, +                               seed = 1234, n.cores = 2,+                               n.celltypes = 4, n.iterations = 500)   conducting the posterior sampling...[>                                       ] Finish 0.00k/0.50k iterations.[====>                                   ] Finish 0.05k/0.50k iterations.[========>                               ] Finish 0.10k/0.50k iterations.[============>                           ] Finish 0.15k/0.50k iterations.[================>                       ] Finish 0.20k/0.50k iterations.[====================>                   ] Finish 0.25k/0.50k iterations.[========================>               ] Finish 0.30k/0.50k iterations.[============================>           ] Finish 0.35k/0.50k iterations.[================================>       ] Finish 0.40k/0.50k iterations.[====================================>   ] Finish 0.45k/0.50k iterations.[========================================] Finish 0.50k/0.50k iterations.   The MCMC sampling takes: 0.25 mins   conducting the posterior inference...   Posterior inference takes: 0.006 mins> > ################################################> # Extract Estimates from the BUSseqfits Object #> ################################################> > #return cell type indicators> w.est <- celltypes(BUSseqfits_res)Batch 1 cells' cell type indicators: 1,1,1... ...Batch 2 cells' cell type indicators: 1,1,1... ...The output format is an N-dimensional verctor.> > #return the intercept and odds ratio of the logistic regression> #for dropout events> gamma.est <- dropout_coefficient_values(BUSseqfits_res)The output format is a matrix.Each row represents a batch, the first column corresponds to intercept and the second column is the odd ratio.> > #return the log-scale baseline expression values> alpha.est <-  baseline_expression_values(BUSseqfits_res)The output format is a vector.> > #return the cell-type effects> beta.est <- celltype_effects(BUSseqfits_res)The output format is a matrix.Each row represents a gene, and each column corresponds to a cell type.> > #return the mean expression levels> mu.est <- celltype_mean_expression(BUSseqfits_res)The output format is a matrix.Each row represents a gene, and each column corresponds to a cell type.> > #return the cell-specific global effects> delta.est <- cell_effect_values(BUSseqfits_res)The output format is an N-dimensional vector.> > #return the location batch effects> nu.est <- location_batch_effects(BUSseqfits_res)The output format is a matrix.Each row represents a gene, and each column corresponds to a batch.> > #return the overdispersion parameters> phi.est <- overdispersions(BUSseqfits_res)The output format is a matrix.Each row represents a gene, and each column corresponds to a batch.> > #return the intrinsic gene indices> D.est <- intrinsic_genes_BUSseq(BUSseqfits_res)> > #return the BIC value> BIC <- BIC_BUSseq(BUSseqfits_res)BIC is 460947.370514477The output is a scalar.> > #return the raw read count matrix> CountData_raw <- raw_read_counts(BUSseqfits_res)The output format is a matrix, in which each row represents a gene and each column does a cell.> > #return the imputed read count matrix> CountData_imputed <- imputed_read_counts(BUSseqfits_res)The output format is a matrix, in which each row represents a gene and each column does a cell.> > #return the corrected read count matrix> BUSseqfits_res <- corrected_read_counts(BUSseqfits_res)   correcting read counts...The corrected read count matrix is added into the output "SingleCellExperiment" object.> > #################> # Visualization #> #################> #generate the heatmap of raw read count data> heatmap_data_BUSseq(BUSseqfits_res, project_name="Heatmap_raw")null device           1 > > #generate the heatmap of imputed read count data> heatmap_data_BUSseq(BUSseqfits_res, data_type = "Imputed",+                     project_name="Heatmap_imputed")null device           1 > > #generate the heatmap of corrected read count data> heatmap_data_BUSseq(BUSseqfits_res, data_type = "Corrected", +                     project_name="Heatmap_corrected")null device           1 > > proc.time()   user  system elapsed  38.028   0.727  24.214