Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-08-04 11:48 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1186/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mastR 1.8.0  (landing page)
Jinjin Chen
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/mastR
git_branch: RELEASE_3_21
git_last_commit: 8e934fb
git_last_commit_date: 2025-04-15 13:14:09 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for mastR on kunpeng2

To the developers/maintainers of the mastR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mastR.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.

raw results


Summary

Package: mastR
Version: 1.8.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:mastR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mastR_1.8.0.tar.gz
StartedAt: 2025-08-01 11:09:00 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 11:49:00 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 2400.3 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: mastR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:mastR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mastR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mastR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mastR/DESCRIPTION’ ... OK
* this is package ‘mastR’ version ‘1.8.0’
* 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 ‘mastR’ 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'DEGs_Group.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'DEGs_RP.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'de_analysis.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'process_data.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'select_sig.Rd':
  ‘[limma:ebayes]{limma::treat()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
plot_diagnostics  15.953  0.902  16.890
sig_gseaplot      11.773  1.406  12.327
get_panglao_sig    5.763  1.386  12.376
filter_subset_sig  5.186  0.103   5.302
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

mastR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL mastR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘mastR’ ...
** this is package ‘mastR’ version ‘1.8.0’
** 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 (mastR)

Tests output

mastR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(mastR)

> 
> test_check("mastR")
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2787         3348       3847   2869   1903
NotSig           2593         5434      10908  43672  45202
Up              44665        41263      35290   3504   2940
       NK-Others
Down          90
NotSig     49003
Up           952
       NK-Others
Down       29581
NotSig     17543
Up          2921
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2787         3348       3847   2869   1903
NotSig           2593         5434      10908  43672  45202
Up              44665        41263      35290   3504   2940
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2787         3348       3847   2869   1903
NotSig           2593         5434      10908  43672  45202
Up              44665        41263      35290   3504   2940
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   2089
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             3056         2843       2174   1824   1444
NotSig           1246         2669       4189   4576   5527
Up               3926         2716       1865   1828   1257
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             3629         3510       2668   2189   1728
NotSig           1957         3500       5403   5947   7039
Up               4714         3290       2229   2164   1533
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4076         4049       3299   2894   2356
NotSig           1344         2476       4064   4565   5764
Up               4991         3886       3048   2952   2291
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
All samples in sig_data are used!
All samples in bg_data are used!
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
see ?depmap and browseVignettes('depmap') for documentation
loading from cache
see ?depmap and browseVignettes('depmap') for documentation
loading from cache
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'select()' returned 1:many mapping between keys and columns

using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3944       3145   2695   2152
NotSig           1483         2684       4417   4990   6187
Up               4925         3791       2857   2734   2080
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...

Example timings

mastR.Rcheck/mastR-Ex.timings

nameusersystemelapsed
ccle_2_wide0.3040.0200.324
de_analysis4.6030.0844.697
filter_subset_sig5.1860.1035.302
get_de_table2.7770.0082.791
get_degs3.8490.0803.937
get_gsc_sig0.0180.0000.019
get_lm_sig0.0140.0000.015
get_panglao_sig 5.763 1.38612.376
gls2gsc0.0110.0000.011
gsc_plot0.9530.0881.043
list_panglao_organs0.0980.0194.811
list_panglao_types0.1090.0132.312
merge_markers0.0210.0120.033
pca_matrix_plot4.0490.2434.303
plot_diagnostics15.953 0.90216.890
plot_mean_var3.3040.0363.347
process_data2.4610.0322.497
pseudo_sample_list0.1670.0000.167
pseudo_samples0.0590.0040.063
remove_bg_exp1.2450.0201.268
remove_bg_exp_mat1.3820.0081.394
select_sig3.0030.0083.018
sig_boxplot1.1030.0041.109
sig_gseaplot11.773 1.40612.327
sig_heatmap3.4570.1843.646
sig_rankdensity_plot2.0730.0242.101
sig_scatter_plot2.3830.0952.483