Yingxin Lin
| Snapshot Date: 2022-01-03 13:55:13 -0500 (Mon, 03 Jan 2022) |
| git_url: https://git.bioconductor.org/packages/scMerge |
| git_branch: master |
| git_last_commit: 04ba008 |
| git_last_commit_date: 2021-10-26 12:51:33 -0500 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-01-04 11:06:49 -0500 (Tue, 04 Jan 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2021-11-10 r81171) -- "Unsuffered Consequences" | 4307 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4044 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences" | 4122 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the scMerge package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scMerge.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1722/2072 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scMerge 1.11.0 (landing page) Yingxin Lin
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: scMerge |
| Version: 1.11.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scMerge.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scMerge_1.11.0.tar.gz |
| StartedAt: 2022-01-03 20:03:16 -0500 (Mon, 03 Jan 2022) |
| EndedAt: 2022-01-03 20:06:49 -0500 (Mon, 03 Jan 2022) |
| EllapsedTime: 212.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scMerge.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scMerge.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scMerge_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scMerge.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 'scMerge/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scMerge' version '1.11.0' * 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 * 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 Namespace in Imports field not imported from: '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 files in 'vignettes' ... OK * 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: 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/scMerge.Rcheck/00check.log' for details.
scMerge.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scMerge
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'scMerge' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scMerge'
finding HTML links ... done
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
* DONE (scMerge)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'scry' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'velociraptor' is missing or broken
done
scMerge.Rcheck/tests/testthat.Rout
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)
> 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] 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 2 1 2
3 1 1 3
4 1 2 1
5 3 2 2
6 2 2 3
Dimension of the replicates mapping matrix:
[1] 200 3
Could not find a batch column in colData(sce_combine)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 1 1 2
3 2 1 3
4 3 2 1
5 2 2 2
6 1 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 2 1 1
2 1 1 2
3 3 1 3
4 4 2 1
5 1 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 4 2 1
5 1 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 2 1 2
3 1 1 3
4 1 2 1
5 3 2 2
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 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 2 1 1
2 1 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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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
>
> proc.time()
user system elapsed
29.51 2.50 32.10
scMerge.Rcheck/scMerge-Ex.timings
| name | user | system | elapsed | |
| fastRUVIII | 1.18 | 0.01 | 1.19 | |
| ruvSimulate | 1.71 | 0.17 | 1.89 | |
| scMerge | 2.25 | 0.22 | 2.47 | |
| scRUVIII | 1.10 | 0.14 | 1.23 | |
| scRUVg | 0.01 | 0.00 | 0.02 | |
| scReplicate | 1.08 | 0.02 | 1.09 | |
| scSEGIndex | 2.67 | 0.03 | 2.70 | |
| sce_cbind | 0.69 | 0.00 | 0.69 | |