Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 258/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUSseq 1.11.0 (landing page) Fangda Song
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: BUSseq |
Version: 1.11.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BUSseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BUSseq_1.11.0.tar.gz |
StartedAt: 2024-08-27 03:06:53 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 03:10:45 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 231.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUSseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:BUSseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BUSseq_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BUSseq.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BUSseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BUSseq’ version ‘1.11.0’ * 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++ (GCC) 10.3.1’ * 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 ... NOTE Note: 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/BUSseq.Rcheck/00check.log’ for details.
BUSseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BUSseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘BUSseq’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ /home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -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:2674:7: warning: variable ‘All_Drop’ set but not used [-Wunused-but-set-variable] 2674 | bool All_Drop = true; | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c rngstream.cpp -o rngstream.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o BUSseq.so BUSseq.o rngstream.o -fopenmp -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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)
BUSseq.Rcheck/tests/BUSseq_example.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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, 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 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: 0.356 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 460947.370514477 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 53.372 0.555 33.772
BUSseq.Rcheck/BUSseq-Ex.timings
name | user | system | elapsed | |
BIC_BUSseq | 0.201 | 0.028 | 0.229 | |
BUSseq-package | 0 | 0 | 0 | |
BUSseq_MCMC | 0 | 0 | 0 | |
BUSseqfits_example | 0 | 0 | 0 | |
baseline_expression_values | 0.077 | 0.016 | 0.093 | |
cell_effect_values | 0.173 | 0.004 | 0.178 | |
celltype_effects | 0.086 | 0.000 | 0.087 | |
celltype_mean_expression | 0.087 | 0.000 | 0.087 | |
celltypes | 0.086 | 0.000 | 0.086 | |
corrected_read_counts | 1.540 | 0.024 | 1.567 | |
dropout_coefficient_values | 0.087 | 0.004 | 0.091 | |
heatmap_data_BUSseq | 0.432 | 0.024 | 0.515 | |
imputed_read_counts | 0.234 | 0.008 | 0.242 | |
intrinsic_genes_BUSseq | 0.099 | 0.000 | 0.099 | |
location_batch_effects | 0.080 | 0.004 | 0.084 | |
overdispersions | 0.084 | 0.000 | 0.085 | |
raw_read_counts | 0.227 | 0.004 | 0.232 | |