Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:03 -0400 (Fri, 31 May 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" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings M3Drop_1.30.0.tar.gz |
StartedAt: 2024-05-31 05:06:05 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 05:12:43 -0400 (Fri, 31 May 2024) |
EllapsedTime: 398.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: M3Drop.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings M3Drop_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/M3Drop.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed NewSimulations 95.241 1.384 96.628 Imputation 39.604 0.160 39.765 M3D_getmarkers 31.836 0.204 32.042 M3D_ConverData 6.172 0.168 6.340 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/M3Drop.Rcheck/00check.log’ for details.
M3Drop.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL M3Drop ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 | 3.540 | 0.144 | 3.687 | |
Consensus_FS | 0.273 | 0.016 | 0.288 | |
Fitting_Dropout_Models | 0 | 0 | 0 | |
Imputation | 39.604 | 0.160 | 39.765 | |
M3D_Clean_Data | 1.268 | 0.116 | 1.384 | |
M3D_ConverData | 6.172 | 0.168 | 6.340 | |
M3D_Differential_Expression | 1.866 | 0.060 | 1.927 | |
M3D_Dropout_Models | 1.054 | 0.040 | 1.095 | |
M3D_Expression_Heatmap | 0.474 | 0.000 | 0.474 | |
M3D_Get_Extremes | 2.216 | 0.076 | 2.291 | |
M3D_Get_Heatmap_Cell_Clusters | 0.424 | 0.004 | 0.428 | |
M3D_Simulations | 0 | 0 | 0 | |
M3D_Test_Shift | 1.349 | 0.016 | 1.366 | |
M3D_ThreeSet_Venn | 0.322 | 0.000 | 0.323 | |
M3D_TraditionalDE | 0.01 | 0.00 | 0.01 | |
M3D_getmarkers | 31.836 | 0.204 | 32.042 | |
M3D_horz_res | 0 | 0 | 0 | |
NBumi_CheckFit | 2.000 | 0.136 | 2.136 | |
NBumi_CoExpression | 0.690 | 0.028 | 0.718 | |
NBumi_CompareModels | 2.722 | 0.072 | 2.794 | |
NBumi_ConvertToInteger | 0.001 | 0.000 | 0.001 | |
NBumi_ConvrtData | 0.277 | 0.008 | 0.286 | |
NBumi_FSDrop | 1.517 | 0.048 | 1.565 | |
NBumi_FSHighVar | 0.639 | 0.016 | 0.655 | |
NBumi_FSOther | 0.011 | 0.000 | 0.011 | |
NBumi_FitDisp | 0.001 | 0.000 | 0.000 | |
NBumi_FitDispVsMean | 0.537 | 0.000 | 0.537 | |
NBumi_FitModel | 0.625 | 0.024 | 0.649 | |
NBumi_HVG | 0.753 | 0.004 | 0.757 | |
NBumi_PearsonResiduals | 1.238 | 0.004 | 1.241 | |
NBumi_TradDE | 0.000 | 0.000 | 0.001 | |
NewSimulations | 95.241 | 1.384 | 96.628 | |
Other_FS | 1.629 | 0.084 | 1.714 | |
PoissonUMIFeatureSelectionDropouts | 0.559 | 0.004 | 0.562 | |
bg__fit_gamma | 0 | 0 | 0 | |
bg__get_stats | 0 | 0 | 0 | |
bg__mean2disp | 0.000 | 0.001 | 0.000 | |
bg__shift_size | 0 | 0 | 0 | |
bg__var_vs_drop | 0 | 0 | 0 | |