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This page was generated on 2025-10-02 12:07 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4576
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1155/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.35.0  (landing page)
Tallulah Andrews
Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 2025)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: devel
git_last_commit: 66aa05f
git_last_commit_date: 2025-04-15 11:06:38 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for M3Drop on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: M3Drop
Version: 1.35.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings M3Drop_1.35.0.tar.gz
StartedAt: 2025-09-30 09:45:09 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 09:53:17 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 487.8 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings M3Drop_1.35.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/M3Drop.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 ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.35.0’
* 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 156.935  0.291 157.638
Imputation      81.783  0.128  82.071
M3D_getmarkers  51.729  0.120  51.991
M3D_ConverData   7.690  0.120   7.827
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/M3Drop.Rcheck/00check.log’
for details.


Installation output

M3Drop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘M3Drop’ ...
** this is package ‘M3Drop’ version ‘1.35.0’
** 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)

Tests output


Example timings

M3Drop.Rcheck/M3Drop-Ex.timings

nameusersystemelapsed
Brennecke_getVariableGenes4.7950.1354.956
Consensus_FS1.6960.0161.716
Fitting_Dropout_Models0.0000.0000.001
Imputation81.783 0.12882.071
M3D_Clean_Data2.2410.0642.310
M3D_ConverData7.6900.1207.827
M3D_Differential_Expression1.7860.0231.814
M3D_Dropout_Models2.0820.0162.104
M3D_Expression_Heatmap0.5960.0080.606
M3D_Get_Extremes3.6320.0163.656
M3D_Get_Heatmap_Cell_Clusters0.5510.0040.556
M3D_Simulations000
M3D_Test_Shift0.8780.0000.881
M3D_ThreeSet_Venn0.3680.0040.372
M3D_TraditionalDE0.0140.0000.015
M3D_getmarkers51.729 0.12051.991
M3D_horz_res000
NBumi_CheckFit3.0150.0883.107
NBumi_CoExpression1.5910.0241.617
NBumi_CompareModels4.7860.0244.820
NBumi_ConvertToInteger0.0010.0000.000
NBumi_ConvrtData0.3620.0120.374
NBumi_FSDrop2.0200.0122.037
NBumi_FSHighVar2.3190.0002.324
NBumi_FSOther0.0140.0000.013
NBumi_FitDisp0.0000.0000.001
NBumi_FitDispVsMean1.3390.0001.341
NBumi_FitModel1.6280.0081.639
NBumi_HVG1.8630.0001.867
NBumi_PearsonResiduals2.4710.0042.481
NBumi_TradDE0.0010.0000.000
NewSimulations156.935 0.291157.638
Other_FS3.1130.0123.132
PoissonUMIFeatureSelectionDropouts1.5960.0401.640
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size0.0000.0010.000
bg__var_vs_drop000