Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1152/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
M3Drop 1.34.0 (landing page) Tallulah Andrews
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the M3Drop package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/M3Drop.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. |
Package: M3Drop |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings M3Drop_1.34.0.tar.gz |
StartedAt: 2025-10-15 02:07:04 -0400 (Wed, 15 Oct 2025) |
EndedAt: 2025-10-15 02:13:05 -0400 (Wed, 15 Oct 2025) |
EllapsedTime: 361.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: M3Drop.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings M3Drop_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/M3Drop.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘M3Drop/DESCRIPTION’ ... OK * this is package ‘M3Drop’ version ‘1.34.0’ * 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 ‘M3Drop’ 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘scater’ 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 ... NOTE M3DropConvertData: no visible global function definition for ‘assays’ NBumiConvertData: no visible global function definition for ‘assays’ bg__filter_cells: no visible binding for global variable ‘x’ bg__get_extreme_residuals: no visible binding for global variable ‘x’ Undefined global functions or variables: assays x * checking Rd files ... NOTE prepare_Rd: NBumi_FSOther.Rd:8-10: Dropping empty section \usage prepare_Rd: NBumi_TradDE.Rd:7-8: Dropping empty section \usage * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed NewSimulations 113.674 1.737 115.700 Imputation 47.736 0.174 48.183 M3D_getmarkers 30.830 0.897 31.794 M3D_ConverData 6.166 0.274 6.503 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/M3Drop.Rcheck/00check.log’ for details.
M3Drop.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL M3Drop ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘M3Drop’ ... ** this is package ‘M3Drop’ version ‘1.34.0’ ** using staged installation ** R ** 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 (M3Drop)
M3Drop.Rcheck/M3Drop-Ex.timings
name | user | system | elapsed | |
Brennecke_getVariableGenes | 4.186 | 0.189 | 4.423 | |
Consensus_FS | 0.321 | 0.022 | 0.345 | |
Fitting_Dropout_Models | 0 | 0 | 0 | |
Imputation | 47.736 | 0.174 | 48.183 | |
M3D_Clean_Data | 2.479 | 0.094 | 2.649 | |
M3D_ConverData | 6.166 | 0.274 | 6.503 | |
M3D_Differential_Expression | 2.617 | 0.108 | 2.759 | |
M3D_Dropout_Models | 1.247 | 0.127 | 1.388 | |
M3D_Expression_Heatmap | 0.800 | 0.014 | 0.818 | |
M3D_Get_Extremes | 2.672 | 0.154 | 2.841 | |
M3D_Get_Heatmap_Cell_Clusters | 0.697 | 0.010 | 0.709 | |
M3D_Simulations | 0 | 0 | 0 | |
M3D_Test_Shift | 0.551 | 0.059 | 0.613 | |
M3D_ThreeSet_Venn | 0.589 | 0.008 | 0.597 | |
M3D_TraditionalDE | 0.012 | 0.001 | 0.013 | |
M3D_getmarkers | 30.830 | 0.897 | 31.794 | |
M3D_horz_res | 0.000 | 0.001 | 0.001 | |
NBumi_CheckFit | 2.525 | 0.134 | 2.665 | |
NBumi_CoExpression | 1.586 | 0.087 | 1.674 | |
NBumi_CompareModels | 2.205 | 0.244 | 2.451 | |
NBumi_ConvertToInteger | 0.001 | 0.000 | 0.000 | |
NBumi_ConvrtData | 0.314 | 0.020 | 0.348 | |
NBumi_FSDrop | 1.869 | 0.116 | 1.986 | |
NBumi_FSHighVar | 0.750 | 0.088 | 0.838 | |
NBumi_FSOther | 0.013 | 0.001 | 0.013 | |
NBumi_FitDisp | 0.000 | 0.001 | 0.000 | |
NBumi_FitDispVsMean | 0.577 | 0.056 | 0.633 | |
NBumi_FitModel | 0.733 | 0.097 | 0.831 | |
NBumi_HVG | 0.920 | 0.133 | 1.053 | |
NBumi_PearsonResiduals | 1.712 | 0.168 | 1.891 | |
NBumi_TradDE | 0.001 | 0.000 | 0.000 | |
NewSimulations | 113.674 | 1.737 | 115.700 | |
Other_FS | 1.855 | 0.037 | 1.894 | |
PoissonUMIFeatureSelectionDropouts | 1.602 | 0.144 | 1.769 | |
bg__fit_gamma | 0.000 | 0.000 | 0.001 | |
bg__get_stats | 0 | 0 | 0 | |
bg__mean2disp | 0 | 0 | 0 | |
bg__shift_size | 0.001 | 0.000 | 0.000 | |
bg__var_vs_drop | 0.000 | 0.000 | 0.001 | |