Kevin Wang
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/scMerge |
| Branch: RELEASE_3_10 |
| Last Commit: b2effcb |
| Last Changed Date: 2019-10-29 13:11:39 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:24 -0400 (Wed, 15 Apr 2020).
| Package 1537/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scMerge 1.2.0 Kevin Wang
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scMerge |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scMerge.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scMerge_1.2.0.tar.gz |
| StartedAt: 2020-04-15 06:26:41 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:33:07 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 385.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scMerge.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scMerge.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings scMerge_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/scMerge.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 'scMerge/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scMerge' version '1.2.0' * 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 ... NOTE Namespaces in Imports field not imported from: 'RcppEigen' 'parallel' 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 ... 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 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/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-3.10-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 ** running examples for arch 'x64' ... OK * 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/scMerge.Rcheck/00check.log' for details.
scMerge.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/scMerge_1.2.0.tar.gz && rm -rf scMerge.buildbin-libdir && mkdir scMerge.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scMerge.buildbin-libdir scMerge_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL scMerge_1.2.0.zip && rm scMerge_1.2.0.tar.gz scMerge_1.2.0.zip
###
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% 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 3383k 100 3383k 0 0 35.2M 0 --:--:-- --:--:-- --:--:-- 37.1M
install for i386
* installing *source* package 'scMerge' ...
** 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:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/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:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcppFastMatrixOp.cpp -o rcppFastMatrixOp.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:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat.h:1:0,
from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h:140:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.10-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++ -std=gnu++11 -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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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++ -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:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/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:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c rcppFastMatrixOp.cpp -o rcppFastMatrixOp.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:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat.h:1:0,
from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h:140:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.10-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++ -std=gnu++11 -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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/scMerge.buildbin-libdir/scMerge/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scMerge' as scMerge_1.2.0.zip
* DONE (scMerge)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'scMerge' successfully unpacked and MD5 sums checked
|
scMerge.Rcheck/tests_i386/testthat.Rout
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.
> library(testthat)
> library(scMerge)
>
> test_check("scMerge")
Dimension of the replicates mapping matrix:
[1] 100 3
Dimension of the replicates mapping matrix:
[1] 100 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 4
Dimension of the replicates mapping matrix:
[1] 200 3
Selecting optimal RUVk
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1 1 2
3 2 1 3
4 1 2 1
5 3 2 2
6 2 2 3
Dimension of the replicates mapping matrix:
[1] 200 3
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 2 1 2
3 1 1 3
4 3 2 1
5 2 2 2
6 1 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 2 1 1
2 3 1 2
3 1 1 3
4 4 2 1
5 5 2 2
6 1 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 2 1 1
2 3 1 2
3 1 1 3
4 4 2 1
5 5 2 2
6 1 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 2 1 1
2 3 1 2
3 1 1 3
4 4 2 1
5 5 2 2
6 1 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 2 1 2
3 1 1 3
4 1 2 1
5 2 2 2
6 3 2 3
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 relevant 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 2 1 2
3 1 1 3
4 1 2 1
5 3 2 2
6 2 2 3
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1
2 2 1 2
3 3 1 3
4 1 2 1
5 4 2 2
6 5 2 3
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1
2 2 1 2
3 3 1 3
4 1 2 1
5 4 2 2
6 5 2 3
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1 1 2
3 2 1 3
4 1 2 1
5 2 2 2
6 3 2 3
7. Performing semi-supervised scMerge with wanted variation
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1 1 2
3 2 1 3
4 3 2 1
5 2 2 2
6 1 2 3
7. Performing semi-supervised scMerge with wanted variation
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
36 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 1 1 1
2 2 1 2
3 3 1 3
4 1 2 1
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
36 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 1 1 1
2 2 1 2
3 3 1 3
4 1 2 1
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
63 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 2 1 2
3 1 1 3
4 2 2 1
5 1 2 2
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
63 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 2 1 1
2 1 1 2
3 3 1 3
4 1 2 1
5 2 2 2
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
24 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 1 1 1
2 2 2 1
3 1 3 1
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
24 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 1 1 1
2 2 2 1
3 1 3 1
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Dimension of the replicates mapping matrix:
[1] 50 3
Dimension of the replicates mapping matrix:
[1] 50 3
Dimension of the replicates mapping matrix:
[1] 50 3
== testthat results ===========================================================
[ OK: 35 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
41.65 2.14 43.98
|
scMerge.Rcheck/tests_x64/testthat.Rout
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.
> library(testthat)
> library(scMerge)
>
> test_check("scMerge")
Dimension of the replicates mapping matrix:
[1] 100 3
Dimension of the replicates mapping matrix:
[1] 100 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 3
Dimension of the replicates mapping matrix:
[1] 200 4
Dimension of the replicates mapping matrix:
[1] 200 3
Selecting optimal RUVk
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1 1 2
3 2 1 3
4 1 2 1
5 3 2 2
6 2 2 3
Dimension of the replicates mapping matrix:
[1] 200 3
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 2 1 2
3 1 1 3
4 3 2 1
5 2 2 2
6 1 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 2 1 1
2 3 1 2
3 1 1 3
4 4 2 1
5 5 2 2
6 1 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 2 1 1
2 3 1 2
3 1 1 3
4 4 2 1
5 5 2 2
6 1 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 2 1 1
2 3 1 2
3 1 1 3
4 4 2 1
5 5 2 2
6 1 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 2 1 2
3 1 1 3
4 1 2 1
5 2 2 2
6 3 2 3
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 relevant 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 2 1 2
3 1 1 3
4 1 2 1
5 3 2 2
6 2 2 3
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1
2 2 1 2
3 3 1 3
4 1 2 1
5 4 2 2
6 5 2 3
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1
2 2 1 2
3 3 1 3
4 1 2 1
5 4 2 2
6 5 2 3
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1 1 2
3 2 1 3
4 1 2 1
5 2 2 2
6 3 2 3
7. Performing semi-supervised scMerge with wanted variation
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant 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 1 1 2
3 2 1 3
4 3 2 1
5 2 2 2
6 1 2 3
7. Performing semi-supervised scMerge with wanted variation
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
36 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 1 1 1
2 2 1 2
3 3 1 3
4 1 2 1
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
36 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 1 1 1
2 2 1 2
3 3 1 3
4 1 2 1
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
63 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 2 1 2
3 1 1 3
4 2 2 1
5 1 2 2
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
63 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 2 1 1
2 1 1 2
3 3 1 3
4 1 2 1
5 2 2 2
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
24 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 1 1 1
2 2 2 1
3 1 3 1
Performing unsupervised scMerge with:
1. No cell type information
2. Cell type indices not relevant here
3. Mutual nearest neighbour matching
4. No supplied marker and no supplied marker_list for MNN clustering
Finding Highly Variable Genes for clustering
24 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 1 1 1
2 2 2 1
3 1 3 1
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Dimension of the replicates mapping matrix:
[1] 50 3
Dimension of the replicates mapping matrix:
[1] 50 3
Dimension of the replicates mapping matrix:
[1] 50 3
== testthat results ===========================================================
[ OK: 35 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
30.17 1.28 31.65
|
|
scMerge.Rcheck/examples_i386/scMerge-Ex.timings
|
scMerge.Rcheck/examples_x64/scMerge-Ex.timings
|