##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUSseq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BUSseq_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BUSseq.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BUSseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUSseq' version '1.1.0'
* 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
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/BUSseq/libs/x64/BUSseq.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 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
  'D:/biocbuild/bbs-3.15-bioc/meat/BUSseq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BUSseq
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BUSseq' ...
** using staged installation
** libs
D:/biocbuild/bbs-3.15-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'
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
     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]
  bool All_Drop = true;
       ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rngstream.cpp -o rngstream.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BUSseq.dll tmp.def BUSseq.o rngstream.o -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-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
  converting help for package 'BUSseq'
    finding HTML links ... done
    BIC_BUSseq                              html  
    BUSseq-package                          html  
    BUSseq_MCMC                             html  
    BUSseqfits_example                      html  
    baseline_expression_values              html  
    cell_effect_values                      html  
    celltype_effects                        html  
    celltype_mean_expression                html  
    celltypes                               html  
    corrected_read_counts                   html  
    dropout_coefficient_values              html  
    heatmap_data_BUSseq                     html  
    imputed_read_counts                     html  
    intrinsic_genes_BUSseq                  html  
    location_batch_effects                  html  
    overdispersions                         html  
    raw_read_counts                         html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'tRNA' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

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: 0.887 mins

   conducting the posterior inference...

   Posterior inference takes: 0.926 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 
 107.84   32.70  116.71