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CHECK report for scMerge on tokay2

This page was generated on 2019-10-16 12:44:13 -0400 (Wed, 16 Oct 2019).

Package 1470/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scMerge 1.0.0
Kevin Wang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/scMerge
Branch: RELEASE_3_9
Last Commit: 74ec5e4
Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scMerge
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scMerge.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scMerge_1.0.0.tar.gz
StartedAt: 2019-10-16 06:55:41 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:01:42 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 360.6 seconds
RetCode: 0
Status:  OK  
CheckDir: scMerge.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scMerge.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scMerge_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scMerge.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scMerge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scMerge' version '1.0.0'
* 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 'scMerge' 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
make_para_gn_parallel: no visible binding for global variable 'i'
Undefined global functions or variables:
  i
* 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-3.9-bioc/R/library/scMerge/libs/i386/scMerge.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-3.9-bioc/R/library/scMerge/libs/x64/scMerge.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
scSEGIndex 0.25   0.03   10.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
scSEGIndex 0.23   0.03   11.53
* 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-3.9-bioc/meat/scMerge.Rcheck/00check.log'
for details.



Installation output

scMerge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/scMerge_1.0.0.tar.gz && rm -rf scMerge.buildbin-libdir && mkdir scMerge.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scMerge.buildbin-libdir scMerge_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scMerge_1.0.0.zip && rm scMerge_1.0.0.tar.gz scMerge_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3353k  100 3353k    0     0  36.2M      0 --:--:-- --:--:-- --:--:-- 38.9M

install for i386

* installing *source* package 'scMerge' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcppFastMatrixOp.cpp -o rcppFastMatrixOp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat.h:1:0,
                 from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h:140:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h:147:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scMerge.dll tmp.def RcppExports.o rcppFastMatrixOp.o test-runner.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/scMerge.buildbin-libdir/00LOCK-scMerge/00new/scMerge/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scMerge'
    finding HTML links ... done
    eigenMatMult                            html  
    eigenResidop                            html  
    example_sce                             html  
    fastRUVIII                              html  
    ruvSimulate                             html  
    scMerge                                 html  
    scRUVIII                                html  
    scRUVg                                  html  
    scReplicate                             html  
    scSEGIndex                              html  
    sce_cbind                               html  
    segList                                 html  
    segList_ensemblGeneID                   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 'scMerge' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcppFastMatrixOp.cpp -o rcppFastMatrixOp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat.h:1:0,
                 from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h:140:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/testthat/include/testthat/testthat.h:147:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
 }
 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scMerge.dll tmp.def RcppExports.o rcppFastMatrixOp.o test-runner.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/scMerge.buildbin-libdir/scMerge/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scMerge' as scMerge_1.0.0.zip
* DONE (scMerge)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'scMerge' successfully unpacked and MD5 sums checked

Tests output

scMerge.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> library(testthat)
> library(scMerge)
> 
> test_check("scMerge")
  group batch cluster
1     3     1       1
2     3     2       3
3     1     1       2
4     1     2       1
5     2     1       3
6     2     2       2
Dimension of the replicates mapping matrix: 
[1] 200   3
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       3
Dimension of the replicates mapping matrix: 
[1] 200   3
  group batch cluster
1     3     1       1
2     3     2       3
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       1
Dimension of the replicates mapping matrix: 
[1] 200 105
Dimension of the replicates mapping matrix: 
[1] 100   3
Dimension of the replicates mapping matrix: 
[1] 100   3
Selecting optimal RUVk 
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       3
5     2     1       3
6     2     2       2
Dimension of the replicates mapping matrix: 
[1] 200 105
Selecting optimal RUVk 
No cell type info, replicate matrix will be used as cell type info 
Performing supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. No mutual nearest neighbour clustering 
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 4. No supplied marker but supplied marker_list for MNN clustering 
    Taking the union of marker_list as the markers 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     1     1       3
2     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     1     1       3
2     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     1     1       3
2     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. Cell type indices 
 3. No mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       2
3     1     1       2
4     1     2       3
5     2     1       3
6     2     2       1
 7. Finishing semi-supervised scMerge with subsets of known cell type 
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       3
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker but supplied marker_list for MNN clustering 
    Taking the union of marker_list as the markers 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     1     1       3
2     2     2       2
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     1     1       2
2     2     2       3
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       2
3     1     1       2
4     1     2       1
5     2     1       3
6     2     2       3
 7. Performing semi-supervised scMerge with wanted variation 
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       3
3     1     1       2
4     1     2       1
5     2     1       3
6     2     2       2
 7. Performing semi-supervised scMerge with wanted variation 

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== testthat results  ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.92    1.65   30.70 

scMerge.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
> library(scMerge)
> 
> test_check("scMerge")
  group batch cluster
1     3     1       1
2     3     2       3
3     1     1       2
4     1     2       1
5     2     1       3
6     2     2       2
Dimension of the replicates mapping matrix: 
[1] 200   3
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       3
Dimension of the replicates mapping matrix: 
[1] 200   3
  group batch cluster
1     3     1       1
2     3     2       3
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       1
Dimension of the replicates mapping matrix: 
[1] 200 105
Dimension of the replicates mapping matrix: 
[1] 100   3
Dimension of the replicates mapping matrix: 
[1] 100   3
Selecting optimal RUVk 
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       3
5     2     1       3
6     2     2       2
Dimension of the replicates mapping matrix: 
[1] 200 105
Selecting optimal RUVk 
No cell type info, replicate matrix will be used as cell type info 
Performing supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. No mutual nearest neighbour clustering 
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 4. No supplied marker but supplied marker_list for MNN clustering 
    Taking the union of marker_list as the markers 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     1     1       3
2     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     1     1       3
2     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. No cell type indices 
 3. Mutual nearest neighbour clustering 
 5. Calculating supervised clustering list 
 6. Create Mutual Nearest Clusters. Preview cells-to-cell_type matching graph and matrix:
  group batch cluster
1     1     1       3
2     2     2       3
Performing semi-supervised scMerge with: 
 1. Cell type information 
 2. Cell type indices 
 3. No mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       2
3     1     1       2
4     1     2       3
5     2     1       3
6     2     2       1
 7. Finishing semi-supervised scMerge with subsets of known cell type 
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       1
3     1     1       2
4     1     2       2
5     2     1       3
6     2     2       3
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker but supplied marker_list for MNN clustering 
    Taking the union of marker_list as the markers 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     1     1       3
2     2     2       2
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     1     1       2
2     2     2       3
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       2
3     1     1       2
4     1     2       1
5     2     1       3
6     2     2       3
 7. Performing semi-supervised scMerge with wanted variation 
Performing unsupervised scMerge with: 
 1. No cell type information 
 2. Cell type indices not revelant here 
 3. Mutual nearest neighbour matching 
 4. No supplied marker and no supplied marker_list for MNN clustering 
    Finding Highly Variable Genes for clustering 
    75 HVG were found 
 5. PCA and Kmeans clustering will be performed on each batch 
 6. Create Mutual Nearest Clusters. Preview cells-cell_type matching output matrix: 
  group batch cluster
1     3     1       1
2     3     2       3
3     1     1       2
4     1     2       1
5     2     1       3
6     2     2       2
 7. Performing semi-supervised scMerge with wanted variation 

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== testthat results  ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.78    0.95   29.75 

Example timings

scMerge.Rcheck/examples_i386/scMerge-Ex.timings

nameusersystemelapsed
eigenMatMult1.780.001.78
eigenResidop2.000.032.03
fastRUVIII0.330.000.33
ruvSimulate2.670.142.81
scMerge1.890.312.20
scRUVIII2.120.032.16
scRUVg0.050.000.04
scReplicate0.420.000.42
scSEGIndex 0.25 0.0310.33
sce_cbind0.770.030.80

scMerge.Rcheck/examples_x64/scMerge-Ex.timings

nameusersystemelapsed
eigenMatMult1.770.001.88
eigenResidop2.010.022.03
fastRUVIII0.210.030.23
ruvSimulate2.840.093.00
scMerge1.560.101.66
scRUVIII1.250.081.33
scRUVg000
scReplicate0.30.00.3
scSEGIndex 0.23 0.0311.53
sce_cbind0.830.060.89