Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-29 15:06:11 -0500 (Mon, 29 Nov 2021).

CHECK results for scMerge on machv2

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.

raw results

Package 1730/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scMerge 1.10.0  (landing page)
Yingxin Lin
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/scMerge
git_branch: RELEASE_3_14
git_last_commit: 8a5a638
git_last_commit_date: 2021-10-26 12:51:33 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scMerge
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMerge.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMerge_1.10.0.tar.gz
StartedAt: 2021-11-28 21:02:49 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 21:09:10 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 381.5 seconds
RetCode: 0
Status:   OK  
CheckDir: scMerge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMerge.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMerge_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/scMerge.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMerge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scMerge’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
scSEGIndex 10.632 13.301  12.823
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/scMerge.Rcheck/00check.log’
for details.



Installation output

scMerge.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scMerge
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘scMerge’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)

Tests output

scMerge.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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     2     2       2
6     3     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     1     2       1
5     3     2       2
6     2     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     1     1       2
3     2     1       3
4     3     2       1
5     2     2       2
6     1     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     3     1       2
3     1     1       3
4     4     2       1
5     5     2       2
6     1     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     2     1       1
2     3     1       2
3     1     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     2     1       2
3     1     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 
    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 
    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     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 
    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     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 
    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 
 61.471   1.906  63.673 

Example timings

scMerge.Rcheck/scMerge-Ex.timings

nameusersystemelapsed
fastRUVIII1.5580.0231.582
ruvSimulate3.4550.0653.523
scMerge3.6030.0803.896
scRUVIII2.3700.0682.642
scRUVg0.0220.0010.024
scReplicate0.6850.0330.719
scSEGIndex10.63213.30112.823
sce_cbind2.4850.1422.628