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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 1137/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.33.0  (landing page)
Tallulah Andrews
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: devel
git_last_commit: a036ab7
git_last_commit_date: 2024-10-29 10:15:21 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for M3Drop on nebbiolo1

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: 1.33.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings M3Drop_1.33.0.tar.gz
StartedAt: 2025-03-13 23:23:20 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 23:29:54 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 393.7 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings M3Drop_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/M3Drop.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.33.0’
* 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 95.125  1.428  96.558
Imputation     39.623  0.204  39.830
M3D_getmarkers 31.616  0.316  31.932
M3D_ConverData  5.001  0.148   5.148
* 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-3.21-bioc/meat/M3Drop.Rcheck/00check.log’
for details.


Installation output

M3Drop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘M3Drop’ ...
** this is package ‘M3Drop’ version ‘1.33.0’
** 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_getVariableGenes3.3320.1613.493
Consensus_FS0.2850.0120.298
Fitting_Dropout_Models000
Imputation39.623 0.20439.830
M3D_Clean_Data1.2900.0911.381
M3D_ConverData5.0010.1485.148
M3D_Differential_Expression2.0870.0612.148
M3D_Dropout_Models0.9710.0401.010
M3D_Expression_Heatmap0.4720.0040.474
M3D_Get_Extremes2.1390.0282.165
M3D_Get_Heatmap_Cell_Clusters0.4300.0030.432
M3D_Simulations0.0000.0000.001
M3D_Test_Shift0.5640.0070.571
M3D_ThreeSet_Venn0.3190.0030.328
M3D_TraditionalDE0.0090.0000.009
M3D_getmarkers31.616 0.31631.932
M3D_horz_res000
NBumi_CheckFit1.3520.1001.453
NBumi_CoExpression1.2200.1311.350
NBumi_CompareModels1.9860.0172.003
NBumi_ConvertToInteger000
NBumi_ConvrtData0.2110.0030.213
NBumi_FSDrop0.8210.0000.820
NBumi_FSHighVar0.6510.0000.652
NBumi_FSOther0.0080.0010.009
NBumi_FitDisp0.0000.0000.001
NBumi_FitDispVsMean0.4690.0000.468
NBumi_FitModel1.2200.0031.222
NBumi_HVG0.7080.0010.708
NBumi_PearsonResiduals0.7010.0140.714
NBumi_TradDE000
NewSimulations95.125 1.42896.558
Other_FS1.7320.1271.859
PoissonUMIFeatureSelectionDropouts0.5660.0050.571
bg__fit_gamma000
bg__get_stats0.0010.0000.000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop0.0000.0000.001