Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 |
Package 1859/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scMerge 1.21.0 (landing page) Yingxin Lin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scMerge package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: scMerge |
Version: 1.21.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scMerge.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scMerge_1.21.0.tar.gz |
StartedAt: 2024-08-27 08:52:58 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 09:03:39 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 641.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scMerge.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:scMerge.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scMerge_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scMerge.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scMerge/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scMerge’ version ‘1.21.0’ * 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 code 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) scMerge.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) scMerge.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) scMerge2.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) scMerge2.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) scMerge2.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly * 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 scMerge2h 19.065 0.128 19.231 scSEGIndex 7.556 9.530 10.287 getAdjustedMat 5.532 0.048 5.595 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/scMerge.Rcheck/00check.log’ for details.
scMerge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL scMerge ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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)
scMerge.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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] 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 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)[1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 89 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 86 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 100 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 1, data1" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 89 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 1, data2" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 86 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 2, data1" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 100 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 89 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 117 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 1, data1" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 89 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 2, data1" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 117 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 86 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 101 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 1, data1" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 1, data2" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 1, data3" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 1, data4" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 50 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 2, data1" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 86 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" [1] "Hierarchical merging level 3, data1" [1] "Cluster within batch" [1] "Normalising data" [1] "Constructing pseudo-bulk" Dimension of pseudo-bulk expression: [1] 1047 101 [1] "Identifying MNC using pseudo-bulk:" [1] "Running RUV" 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 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 2 1 2 3 1 1 3 4 1 2 1 5 2 2 2 6 3 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 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 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 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 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. 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|======================================================================| 100% [ FAIL 0 | WARN 85 | SKIP 0 | PASS 42 ] [ FAIL 0 | WARN 85 | SKIP 0 | PASS 42 ] > > proc.time() user system elapsed 222.991 2.007 225.440
scMerge.Rcheck/scMerge-Ex.timings
name | user | system | elapsed | |
fastRUVIII | 1.786 | 0.004 | 1.792 | |
getAdjustedMat | 5.532 | 0.048 | 5.595 | |
ruvSimulate | 2.419 | 0.032 | 2.463 | |
scMerge | 2.911 | 0.016 | 2.933 | |
scMerge2 | 4.752 | 0.032 | 4.795 | |
scMerge2h | 19.065 | 0.128 | 19.231 | |
scRUVIII | 2.289 | 0.036 | 2.329 | |
scRUVg | 0.043 | 0.004 | 0.047 | |
scReplicate | 0.683 | 0.004 | 0.688 | |
scSEGIndex | 7.556 | 9.530 | 10.287 | |
sce_cbind | 1.195 | 0.083 | 1.282 | |