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This page was generated on 2025-09-15 12:03 -0400 (Mon, 15 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 1150/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.35.0  (landing page)
Tallulah Andrews
Snapshot Date: 2025-09-14 13:45 -0400 (Sun, 14 Sep 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 nebbiolo2

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.

raw results


Summary

Package: M3Drop
Version: 1.35.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings M3Drop_1.35.0.tar.gz
StartedAt: 2025-09-15 01:00:36 -0400 (Mon, 15 Sep 2025)
EndedAt: 2025-09-15 01:08:16 -0400 (Mon, 15 Sep 2025)
EllapsedTime: 460.6 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --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 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 114.083  1.465 115.617
Imputation      47.518  0.126  47.791
M3D_getmarkers  34.377  0.384  34.808
M3D_ConverData   5.619  0.169   5.789
* 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-3.22-bioc/meat/M3Drop.Rcheck/00check.log’
for details.


Installation output

M3Drop.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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_getVariableGenes3.7100.1713.899
Consensus_FS0.2630.0000.263
Fitting_Dropout_Models000
Imputation47.518 0.12647.791
M3D_Clean_Data1.3970.1051.502
M3D_ConverData5.6190.1695.789
M3D_Differential_Expression1.3780.0721.450
M3D_Dropout_Models1.6550.0281.683
M3D_Expression_Heatmap0.5110.0030.514
M3D_Get_Extremes2.3880.0432.447
M3D_Get_Heatmap_Cell_Clusters0.4350.0030.437
M3D_Simulations0.0010.0000.000
M3D_Test_Shift0.6070.0040.611
M3D_ThreeSet_Venn0.3350.0020.337
M3D_TraditionalDE0.0110.0000.011
M3D_getmarkers34.377 0.38434.808
M3D_horz_res000
NBumi_CheckFit2.2840.1482.461
NBumi_CoExpression0.7920.0410.853
NBumi_CompareModels3.0610.0683.133
NBumi_ConvertToInteger0.0010.0000.001
NBumi_ConvrtData0.2180.0050.223
NBumi_FSDrop0.9000.0430.943
NBumi_FSHighVar1.3670.0041.375
NBumi_FSOther0.0080.0000.008
NBumi_FitDisp000
NBumi_FitDispVsMean0.5150.0000.515
NBumi_FitModel0.7000.0210.721
NBumi_HVG0.8510.0070.858
NBumi_PearsonResiduals1.4580.0011.462
NBumi_TradDE000
NewSimulations114.083 1.465115.617
Other_FS1.8020.1111.918
PoissonUMIFeatureSelectionDropouts0.6040.0400.643
bg__fit_gamma000
bg__get_stats000
bg__mean2disp0.0010.0000.000
bg__shift_size0.0000.0000.001
bg__var_vs_drop000