Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1136/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
M3Drop 1.30.0 (landing page) Tallulah Andrews
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.30.0 |
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_1.30.0.tar.gz |
StartedAt: 2024-06-24 06:47:32 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 06:58:58 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 686.2 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_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/M3Drop.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘M3Drop/DESCRIPTION’ ... OK * this is package ‘M3Drop’ version ‘1.30.0’ * 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 160.626 4.300 217.367 M3D_getmarkers 59.287 2.425 91.541 Imputation 57.398 1.070 80.310 M3D_ConverData 7.872 0.447 12.235 Brennecke_getVariableGenes 4.114 0.309 6.178 * 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-3.19-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/4.4-x86_64/Resources/library’ * installing *source* package ‘M3Drop’ ... ** 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 | 4.114 | 0.309 | 6.178 | |
Consensus_FS | 0.407 | 0.037 | 0.632 | |
Fitting_Dropout_Models | 0.001 | 0.000 | 0.000 | |
Imputation | 57.398 | 1.070 | 80.310 | |
M3D_Clean_Data | 1.624 | 0.090 | 2.322 | |
M3D_ConverData | 7.872 | 0.447 | 12.235 | |
M3D_Differential_Expression | 1.755 | 0.097 | 2.818 | |
M3D_Dropout_Models | 1.686 | 0.118 | 2.521 | |
M3D_Expression_Heatmap | 0.692 | 0.023 | 0.985 | |
M3D_Get_Extremes | 1.714 | 0.164 | 2.852 | |
M3D_Get_Heatmap_Cell_Clusters | 0.645 | 0.025 | 1.079 | |
M3D_Simulations | 0 | 0 | 0 | |
M3D_Test_Shift | 1.176 | 0.084 | 1.768 | |
M3D_ThreeSet_Venn | 0.411 | 0.014 | 0.580 | |
M3D_TraditionalDE | 0.014 | 0.001 | 0.021 | |
M3D_getmarkers | 59.287 | 2.425 | 91.541 | |
M3D_horz_res | 0.000 | 0.001 | 0.000 | |
NBumi_CheckFit | 2.642 | 0.240 | 4.569 | |
NBumi_CoExpression | 1.184 | 0.058 | 1.679 | |
NBumi_CompareModels | 3.343 | 0.178 | 4.757 | |
NBumi_ConvertToInteger | 0.001 | 0.000 | 0.001 | |
NBumi_ConvrtData | 0.493 | 0.024 | 0.698 | |
NBumi_FSDrop | 1.434 | 0.062 | 2.189 | |
NBumi_FSHighVar | 1.140 | 0.056 | 1.578 | |
NBumi_FSOther | 0.016 | 0.002 | 0.022 | |
NBumi_FitDisp | 0.000 | 0.001 | 0.001 | |
NBumi_FitDispVsMean | 0.953 | 0.043 | 1.298 | |
NBumi_FitModel | 1.144 | 0.037 | 1.555 | |
NBumi_HVG | 1.829 | 0.067 | 2.471 | |
NBumi_PearsonResiduals | 1.218 | 0.078 | 1.716 | |
NBumi_TradDE | 0 | 0 | 0 | |
NewSimulations | 160.626 | 4.300 | 217.367 | |
Other_FS | 1.370 | 0.049 | 1.762 | |
PoissonUMIFeatureSelectionDropouts | 1.699 | 0.150 | 2.367 | |
bg__fit_gamma | 0.000 | 0.000 | 0.001 | |
bg__get_stats | 0.000 | 0.000 | 0.001 | |
bg__mean2disp | 0.000 | 0.001 | 0.001 | |
bg__shift_size | 0 | 0 | 0 | |
bg__var_vs_drop | 0 | 0 | 0 | |