Package: celda

Version: 1.2.4

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:celda.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings celda_1.2.4.tar.gz

StartedAt: 2020-04-15 01:53:26 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:14:28 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 1262.3 seconds

RetCode: 0

Status:  OK

CheckDir: celda.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:celda.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings celda_1.2.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/celda.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'celda/DESCRIPTION' ... OK
* this is package 'celda' version '1.2.4'
* package encoding: UTF-8
* 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 'celda' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
plotDendro: no visible binding for global variable 'xend'
plotDendro: no visible binding for global variable 'y'
plotDendro: no visible binding for global variable 'label'
plotDimReduceCluster: no visible binding for global variable 'Cluster'
Undefined global functions or variables:
  Cluster label xend y
* 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 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/celda/libs/i386/celda.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/celda/libs/x64/celda.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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
findMarkers              98.72   6.84  105.78
getDecisions             87.02   5.90   92.93
plotDendro               84.28   5.50   89.84
geneSetEnrich            15.34   0.35   15.69
plotDimReduceGrid         9.97   0.11   10.08
recursiveSplitCell        8.69   0.41    9.09
celdaCGMod                7.65   0.23    7.91
recursiveSplitModule      7.30   0.25    7.57
celda_CG                  5.52   0.02    5.53
celdaTsne-celda_C-method  5.22   0.09    5.31
celdaCGGridSearchRes      1.38   0.05   52.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
findMarkers          90.07   5.20   95.32
getDecisions         74.03   5.05   79.08
plotDendro           68.12   5.35   73.49
geneSetEnrich        11.93   0.14   12.06
plotDimReduceGrid     9.16   0.09    9.25
recursiveSplitCell    8.26   0.03    8.29
recursiveSplitModule  7.11   0.00    7.11
celdaCGMod            6.29   0.06    6.34
celdaCGGridSearchRes  1.40   0.01   43.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/celda.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/celda_1.2.4.tar.gz && rm -rf celda.buildbin-libdir && mkdir celda.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=celda.buildbin-libdir celda_1.2.4.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL celda_1.2.4.zip && rm celda_1.2.4.tar.gz celda_1.2.4.zip
###
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100  312k  100  312k    0     0  2218k      0 --:--:-- --:--:-- --:--:-- 2278k

install for i386

* installing *source* package 'celda' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c eigenMatMultInt.cpp -o eigenMatMultInt.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c matrixNorm.cpp -o matrixNorm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrixSums.c -o matrixSums.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c perplexity.c -o perplexity.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o celda.dll tmp.def RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o perplexity.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/celda.buildbin-libdir/00LOCK-celda/00new/celda/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'celda'
    finding HTML links ... done
    appendCeldaList                         html  
    availableModels                         html  
    bestLogLikelihood-celdaModel-method     html  
    bestLogLikelihood                       html  
    celda                                   html  
    celdaCGGridSearchRes                    html  
    celdaCGMod                              html  
    celdaCGSim                              html  
    celdaCMod                               html  
    celdaCSim                               html  
    celdaGMod                               html  
    celdaGSim                               html  
    celdaGridSearch                         html  
    celdaHeatmap-celda_C-method             html  
    celdaHeatmap-celda_CG-method            html  
    celdaHeatmap-celda_G-method             html  
    celdaHeatmap                            html  
    celdaPerplexity-celdaList-method        html  
    celdaPerplexity                         html  
    celdaProbabilityMap-celda_C-method      html  
    celdaProbabilityMap-celda_CG-method     html  
    celdaProbabilityMap                     html  
    celdaTsne-celda_C-method                html  
    celdaTsne-celda_CG-method               html  
    celdaTsne-celda_G-method                html  
    celdaTsne                               html  
    celdaUmap-celda_C-method                html  
    celdaUmap-celda_CG-method               html  
    celdaUmap-celda_G-method                html  
    celdaUmap                               html  
    celda_C                                 html  
    celda_CG                                html  
    celda_G                                 html  
    clusterProbability-celda_C-method       html  
    clusterProbability-celda_CG-method      html  
    clusterProbability-celda_G-method       html  
    clusterProbability                      html  
    clusters-celdaModel-method              html  
    clusters                                html  
    compareCountMatrix                      html  
    contaminationSim                        html  
    countChecksum-celdaList-method          html  
    countChecksum                           html  
    decontX                                 html  
    differentialExpression                  html  
    distinctColors                          html  
    eigenMatMultInt                         html  
    factorizeMatrix-celda_C-method          html  
    factorizeMatrix-celda_CG-method         html  
    factorizeMatrix-celda_G-method          html  
    factorizeMatrix                         html  
    fastNormProp                            html  
    fastNormPropLog                         html  
    fastNormPropSqrt                        html  
    featureModuleLookup-celda_C-method      html  
    featureModuleLookup-celda_CG-method     html  
    featureModuleLookup-celda_G-method      html  
    featureModuleLookup                     html  
    featureModuleTable                      html  
    findMarkers                             html  
    geneSetEnrich                           html  
    getDecisions                            html  
    logLikelihood                           html  
    logLikelihoodHistory-celdaModel-method
                                            html  
    logLikelihoodHistory                    html  
    logLikelihoodcelda_C                    html  
    logLikelihoodcelda_CG                   html  
    logLikelihoodcelda_G                    html  
    matrixNames-celdaModel-method           html  
    matrixNames                             html  
    moduleHeatmap                           html  
    normalizeCounts                         html  
    params-celdaModel-method                html  
    params                                  html  
    perplexity-celda_C-method               html  
    perplexity-celda_CG-method              html  
    perplexity-celda_G-method               html  
    perplexity                              html  
    plotDendro                              html  
    plotDimReduceCluster                    html  
    plotDimReduceFeature                    html  
    plotDimReduceGrid                       html  
    plotDimReduceModule                     html  
    plotGridSearchPerplexity                html  
    plotGridSearchPerplexitycelda_C         html  
    plotGridSearchPerplexitycelda_CG        html  
    plotGridSearchPerplexitycelda_G         html  
    plotHeatmap                             html  
    recodeClusterY                          html  
    recodeClusterZ                          html  
    recursiveSplitCell                      html  
    recursiveSplitModule                    html  
    resList-celdaList-method                html  
    resList                                 html  
    resamplePerplexity                      html  
    runParams-celdaList-method              html  
    runParams                               html  
    sampleCells                             html  
    sampleLabel-celdaModel-method           html  
    sampleLabel                             html  
    selectBestModel                         html  
    semiPheatmap                            html  
    simulateCells                           html  
    simulateCellscelda_C                    html  
    simulateCellscelda_CG                   html  
    simulateCellscelda_G                    html  
    simulateContaminatedMatrix              html  
    subsetCeldaList                         html  
    topRank                                 html  
    violinPlot                              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

install for x64

* installing *source* package 'celda' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c eigenMatMultInt.cpp -o eigenMatMultInt.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c matrixNorm.cpp -o matrixNorm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrixSums.c -o matrixSums.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c perplexity.c -o perplexity.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o celda.dll tmp.def RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o perplexity.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/celda.buildbin-libdir/celda/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'celda' as celda_1.2.4.zip
* DONE (celda)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'celda' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("celda")
Loading required package: celda
== testthat results  ===========================================================
[ OK: 232 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  68.18    2.25   71.46 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> test_check("celda")
Loading required package: celda
== testthat results  ===========================================================
[ OK: 232 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  64.06    1.14   65.18