Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:43 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for BUSseq on machv2


To the developers/maintainers of the BUSseq package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 232/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUSseq 1.0.0  (landing page)
Fangda Song
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/BUSseq
git_branch: RELEASE_3_14
git_last_commit: aae9920
git_last_commit_date: 2021-10-26 13:10:51 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BUSseq
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUSseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUSseq_1.0.0.tar.gz
StartedAt: 2022-04-12 11:05:48 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 11:10:14 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 266.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BUSseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUSseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUSseq_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BUSseq.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BUSseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSseq’ version ‘1.0.0’
* 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
* 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 R 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 is not available
* 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 in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BUSseq.Rcheck/00check.log’
for details.



Installation output

BUSseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BUSseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BUSseq’ ...
** using staged installation
** libs
/Library/Frameworks/R.framework/Resources/share/make/shlib.mk:10: warning: overriding commands for target `BUSseq.so'
Makevars:9: warning: ignoring old commands for target `BUSseq.so'
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BUSseq.cpp -o BUSseq.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rngstream.cpp -o rngstream.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BUSseq.so BUSseq.o rngstream.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

BUSseq.Rcheck/tests/BUSseq_example.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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: 0.757 mins

   conducting the posterior inference...

   Posterior inference takes: 0.016 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 460939.471305478

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 
 59.120   0.908  60.156 

Example timings

BUSseq.Rcheck/BUSseq-Ex.timings

nameusersystemelapsed
BIC_BUSseq0.3090.0030.312
BUSseq-package0.0000.0000.001
BUSseq_MCMC0.0000.0000.001
BUSseqfits_example0.0000.0010.001
baseline_expression_values0.1900.0090.199
cell_effect_values0.1880.0190.206
celltype_effects0.2550.0230.278
celltype_mean_expression0.2450.0230.268
celltypes0.2180.0220.239
corrected_read_counts1.4210.0601.482
dropout_coefficient_values0.1560.0010.157
heatmap_data_BUSseq0.5960.0370.641
imputed_read_counts0.4730.0160.488
intrinsic_genes_BUSseq0.2110.0010.213
location_batch_effects0.2340.0020.236
overdispersions0.2020.0010.203
raw_read_counts0.4700.0140.485