Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 260/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUSseq 1.12.0 (landing page) Fangda Song
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the BUSseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSseq.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: BUSseq |
Version: 1.12.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUSseq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BUSseq_1.12.0.tar.gz |
StartedAt: 2024-12-19 23:38:55 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:47:04 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 488.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUSseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUSseq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BUSseq_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BUSseq.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BUSseq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BUSseq' version '1.12.0' * 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 whether package 'BUSseq' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 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 ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/BUSseq/libs/x64/BUSseq.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/BUSseq.Rcheck/00check.log' for details.
BUSseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BUSseq ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'BUSseq' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++11 F:/biocbuild/bbs-3.20-bioc/R/share/make/winshlib.mk:16: warning: overriding recipe for target 'BUSseq.dll' Makevars.win:9: warning: ignoring old recipe for target 'BUSseq.dll' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BUSseq.cpp -o BUSseq.o BUSseq.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++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rngstream.cpp -o rngstream.o g++ -shared -s -static-libgcc -o BUSseq.dll tmp.def BUSseq.o rngstream.o -fopenmp -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-BUSseq/00new/BUSseq/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BUSseq)
BUSseq.Rcheck/tests/BUSseq_example.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R 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: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching 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, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase Welcome 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': rowMedians The 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: 1.366 mins conducting the posterior inference... Posterior inference takes: 2.938 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 460947.370514477 The 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 211.70 67.42 269.21
BUSseq.Rcheck/BUSseq-Ex.timings
name | user | system | elapsed | |
BIC_BUSseq | 0.72 | 0.00 | 0.72 | |
BUSseq-package | 0 | 0 | 0 | |
BUSseq_MCMC | 0 | 0 | 0 | |
BUSseqfits_example | 0.00 | 0.02 | 0.02 | |
baseline_expression_values | 0.05 | 0.00 | 0.04 | |
cell_effect_values | 0.06 | 0.00 | 0.06 | |
celltype_effects | 0.08 | 0.00 | 0.08 | |
celltype_mean_expression | 0.09 | 0.00 | 0.09 | |
celltypes | 0.04 | 0.03 | 0.08 | |
corrected_read_counts | 0.89 | 0.10 | 0.98 | |
dropout_coefficient_values | 0.1 | 0.0 | 0.1 | |
heatmap_data_BUSseq | 0.42 | 0.09 | 0.54 | |
imputed_read_counts | 0.23 | 0.03 | 0.27 | |
intrinsic_genes_BUSseq | 0.11 | 0.00 | 0.11 | |
location_batch_effects | 0.08 | 0.02 | 0.09 | |
overdispersions | 0.08 | 0.01 | 0.10 | |
raw_read_counts | 0.25 | 0.07 | 0.31 | |