Jinjin Chen
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/mastR |
| git_branch: devel |
| git_last_commit: 492c795 |
| git_last_commit_date: 2024-10-29 11:20:15 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1155/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mastR 1.7.0 (landing page) Jinjin Chen
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
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. |
| Package: mastR |
| Version: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2024-12-24 08:14:41 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 08:54:42 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: mastR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mastR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mastR/DESCRIPTION’ ... OK
* this is package ‘mastR’ version ‘1.7.0’
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* 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
plot_diagnostics 15.031 0.834 15.901
sig_gseaplot 11.595 1.529 12.305
get_panglao_sig 5.907 0.939 13.222
filter_subset_sig 5.076 0.071 5.162
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
mastR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL mastR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘mastR’ ... ** 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)
mastR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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.
> # 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 61
NotSig 48560
Up 1424
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
Warning: program compiled against libxml 212 using older 211
'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...
mastR.Rcheck/mastR-Ex.timings
| name | user | system | elapsed | |
| ccle_2_wide | 0.343 | 0.000 | 0.344 | |
| de_analysis | 4.684 | 0.116 | 4.816 | |
| filter_subset_sig | 5.076 | 0.071 | 5.162 | |
| get_de_table | 2.711 | 0.016 | 2.734 | |
| get_degs | 2.849 | 0.024 | 2.880 | |
| get_gsc_sig | 0.019 | 0.000 | 0.020 | |
| get_lm_sig | 0.015 | 0.000 | 0.016 | |
| get_panglao_sig | 5.907 | 0.939 | 13.222 | |
| gls2gsc | 0.007 | 0.004 | 0.010 | |
| gsc_plot | 0.933 | 0.071 | 1.007 | |
| list_panglao_organs | 0.096 | 0.045 | 2.039 | |
| list_panglao_types | 0.162 | 0.016 | 2.444 | |
| merge_markers | 0.017 | 0.008 | 0.025 | |
| pca_matrix_plot | 3.410 | 0.295 | 3.713 | |
| plot_diagnostics | 15.031 | 0.834 | 15.901 | |
| plot_mean_var | 3.509 | 0.104 | 3.621 | |
| process_data | 2.597 | 0.048 | 2.651 | |
| pseudo_sample_list | 0.163 | 0.008 | 0.171 | |
| pseudo_samples | 0.057 | 0.004 | 0.061 | |
| remove_bg_exp | 1.216 | 0.032 | 1.252 | |
| remove_bg_exp_mat | 1.361 | 0.012 | 1.376 | |
| select_sig | 2.881 | 0.116 | 3.003 | |
| sig_boxplot | 1.003 | 0.028 | 1.033 | |
| sig_gseaplot | 11.595 | 1.529 | 12.305 | |
| sig_heatmap | 3.574 | 0.434 | 4.020 | |
| sig_rankdensity_plot | 2.285 | 0.148 | 2.439 | |
| sig_scatter_plot | 2.373 | 0.172 | 2.552 | |