| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1420/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| muscat 1.23.2 (landing page) Helena L. Crowell
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the muscat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/muscat.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: muscat |
| Version: 1.23.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings muscat_1.23.2.tar.gz |
| StartedAt: 2025-10-17 11:33:50 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 11:42:16 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 505.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: muscat.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:muscat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings muscat_1.23.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘muscat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscat’ version ‘1.23.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘muscat’ 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 ... NOTE
pbHeatmap: no visible binding for global variable ‘gene’
pbHeatmap: no visible binding for global variable ‘p_adj.loc’
pbHeatmap: no visible binding for global variable ‘logFC’
Undefined global functions or variables:
gene logFC p_adj.loc
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'mmDS.Rd':
‘[limma:dupcor]{duplicateCorrelation}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
pbHeatmap.Rd: HeatmapList-class
prepSCE.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
mmDS 9.715 0.184 9.921
pbHeatmap 9.325 0.095 9.447
simData 9.206 0.076 9.312
prepSim 7.166 0.140 7.322
stagewise_DS_DD 7.104 0.120 7.244
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/muscat.Rcheck/00check.log’
for details.
muscat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL muscat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘muscat’ ... ** this is package ‘muscat’ version ‘1.23.2’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning in check_dep_version(dep_pkg = "TMB") : package version mismatch: glmmTMB was built with TMB package version 1.9.17 Current TMB package version is 1.9.18 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in check_dep_version(dep_pkg = "TMB") : package version mismatch: glmmTMB was built with TMB package version 1.9.17 Current TMB package version is 1.9.18 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** testing if installed package can be loaded from final location Warning in check_dep_version(dep_pkg = "TMB") : package version mismatch: glmmTMB was built with TMB package version 1.9.17 Current TMB package version is 1.9.18 Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information) ** testing if installed package keeps a record of temporary installation path * DONE (muscat)
muscat.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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.
> library(testthat)
> library(muscat)
Warning message:
In check_dep_version(dep_pkg = "TMB") : package version mismatch:
glmmTMB was built with TMB package version 1.9.17
Current TMB package version is 1.9.18
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
>
> test_check("muscat")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 555 ]
>
> proc.time()
user system elapsed
134.917 1.463 136.764
muscat.Rcheck/muscat-Ex.timings
| name | user | system | elapsed | |
| aggregateData | 2.347 | 0.048 | 2.399 | |
| calcExprFreqs | 1.235 | 0.036 | 1.273 | |
| data | 0 | 0 | 0 | |
| gBH | 0.011 | 0.000 | 0.011 | |
| mmDS | 9.715 | 0.184 | 9.921 | |
| pbDS | 1.595 | 0.024 | 1.621 | |
| pbFlatten | 0.915 | 0.004 | 0.921 | |
| pbHeatmap | 9.325 | 0.095 | 9.447 | |
| pbMDS | 1.240 | 0.008 | 1.252 | |
| prepSCE | 0.598 | 0.008 | 0.608 | |
| prepSim | 7.166 | 0.140 | 7.322 | |
| resDS | 2.973 | 0.056 | 3.038 | |
| simData | 9.206 | 0.076 | 9.312 | |
| stagewise_DS_DD | 7.104 | 0.120 | 7.244 | |