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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:monocle.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings monocle_2.23.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/monocle.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 'monocle/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'monocle' version '2.23.2'
* 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 'monocle' 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 ... NOTE
Namespaces in Imports field not imported from:
  'Rcpp' 'biocViews'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign_cell_lineage: no visible global function definition for 'nei'
buildBranchCellDataSet: no visible global function definition for 'nei'
count_leaf_descendents: no visible global function definition for 'nei'
cth_classifier_cds: no visible global function definition for 'nei'
cth_classifier_cell: no visible global function definition for 'nei'
diff_test_helper: no visible binding for global variable 'Size_Factor'
exportCDS: no visible binding for global variable 'use_for_ordering'
extract_good_ordering: no visible global function definition for 'nei'
fit_model_helper: no visible binding for global variable 'Size_Factor'
get_next_node_id: no visible binding for '<<-' assignment to
  'next_node'
get_next_node_id: no visible binding for global variable 'next_node'
make_canonical: no visible global function definition for 'nei'
measure_diameter_path: no visible global function definition for 'nei'
orderCells: no visible binding for '<<-' assignment to 'next_node'
plot_multiple_branches_pseudotime: no visible binding for global
  variable 'pseudocount'
plot_multiple_branches_pseudotime: no visible binding for global
  variable 'Branch'
project2MST: no visible global function definition for 'nei'
reverseEmbeddingCDS : <anonymous>: no visible global function
  definition for 'quantile'
Undefined global functions or variables:
  Branch Size_Factor nei next_node pseudocount quantile
  use_for_ordering
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/monocle/libs/x64/monocle.dll':
  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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/monocle.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL monocle
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'monocle' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c clustering.cpp -o clustering.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o monocle.dll tmp.def RcppExports.o clustering.o -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-monocle/00new/monocle/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 'monocle'
    finding HTML links ... done
    BEAM                                    html  
    CellDataSet-methods                     html  
    CellDataSet                             html  
    CellType                                html  
    CellTypeHierarchy                       html  
    addCellType                             html  
    branchTest                              html  
    buildBranchCellDataSet                  html  
    calABCs                                 html  
    calILRs                                 html  
    calibrate_per_cell_total_proposal       html  
    cellPairwiseDistances-set               html  
    cellPairwiseDistances                   html  
    clusterCells                            html  
    clusterGenes                            html  
    compareModels                           html  
    detectBifurcationPoint                  html  
    detectGenes                             html  
    diff_test_helper                        html  
    differentialGeneTest                    html  
    dispersionTable                         html  
    estimateDispersionsForCellDataSet       html  
    estimateSizeFactorsForMatrix            html  
    estimate_t                              html  
    exportCDS                               html  
    extract_good_branched_ordering          html  
    fitModel                                html  
    fit_model_helper                        html  
    genSmoothCurveResiduals                 html  
    genSmoothCurves                         html  
    get_classic_muscle_markers              html  
    importCDS                               html  
    load_HSMM                               html  
    load_HSMM_markers                       html  
    load_lung                               html  
    markerDiffTable                         html  
    mcesApply                               html  
    minSpanningTree-set                     html  
    minSpanningTree                         html  
    newCellDataSet                          html  
    newCellTypeHierarchy                    html  
    orderCells                              html  
    order_p_node                            html  
    package-deprecated                      html  
    plot_cell_clusters                      html  
    plot_cell_trajectory                    html  
    plot_clusters                           html  
    plot_coexpression_matrix                html  
    plot_complex_cell_trajectory            html  
    plot_genes_branched_heatmap             html  
    plot_genes_branched_pseudotime          html  
    plot_genes_in_pseudotime                html  
    plot_genes_jitter                       html  
    plot_genes_positive_cells               html  
    plot_genes_violin                       html  
    plot_multiple_branches_heatmap          html  
    plot_multiple_branches_pseudotime       html  
    plot_ordering_genes                     html  
    plot_pc_variance_explained              html  
    plot_pseudotime_heatmap                 html  
    plot_rho_delta                          html  
    pq_helper                               html  
    reduceDimension                         html  
    reducedDimA-set                         html  
    reducedDimA                             html  
    reducedDimK-set                         html  
    reducedDimK                             html  
    reducedDimS-set                         html  
    reducedDimS                             html  
    reducedDimW-set                         html  
    reducedDimW                             html  
    relative2abs                            html  
    residualMatrix                          html  
    responseMatrix                          html  
    selectTopMarkers                        html  
    setOrderingFilter                       html  
    spike_df                                html  
    vstExprs                                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 (monocle)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'macat' 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.

> library(testthat)
> #test_check("monocle")
> 
> proc.time()
   user  system elapsed 
   0.23    0.06    0.28