Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1152/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.34.0  (landing page)
Tallulah Andrews
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: RELEASE_3_21
git_last_commit: c09d743
git_last_commit_date: 2025-04-15 11:06:38 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for M3Drop on kjohnson3

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: 1.34.0
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_1.34.0.tar.gz
StartedAt: 2025-04-21 20:05:18 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 20:07:19 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 120.6 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/M3Drop.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.34.0’
* 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 38.250  0.569  38.877
Imputation     17.939  0.042  17.991
M3D_getmarkers  9.799  0.370  10.198
* 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-3.21-bioc/meat/M3Drop.Rcheck/00check.log’
for details.


Installation output

M3Drop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘M3Drop’ ...
** this is package ‘M3Drop’ version ‘1.34.0’
** 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_getVariableGenes1.4480.0741.526
Consensus_FS0.1110.0130.124
Fitting_Dropout_Models000
Imputation17.939 0.04217.991
M3D_Clean_Data0.6910.0300.728
M3D_ConverData2.2230.0812.327
M3D_Differential_Expression0.4790.0180.509
M3D_Dropout_Models0.7660.0300.804
M3D_Expression_Heatmap0.2520.0030.256
M3D_Get_Extremes0.9590.0511.011
M3D_Get_Heatmap_Cell_Clusters0.2260.0050.232
M3D_Simulations000
M3D_Test_Shift0.1850.0180.204
M3D_ThreeSet_Venn0.1860.0020.190
M3D_TraditionalDE0.0060.0010.007
M3D_getmarkers 9.799 0.37010.198
M3D_horz_res000
NBumi_CheckFit0.8530.0600.915
NBumi_CoExpression0.2710.0280.300
NBumi_CompareModels1.0130.0881.116
NBumi_ConvertToInteger000
NBumi_ConvrtData0.0820.0060.089
NBumi_FSDrop0.3520.0450.399
NBumi_FSHighVar0.5230.0360.561
NBumi_FSOther0.0060.0000.006
NBumi_FitDisp000
NBumi_FitDispVsMean0.1950.0160.210
NBumi_FitModel0.2540.0290.283
NBumi_HVG0.3020.0440.347
NBumi_PearsonResiduals0.5610.0420.604
NBumi_TradDE000
NewSimulations38.250 0.56938.877
Other_FS0.9080.0510.959
PoissonUMIFeatureSelectionDropouts0.2080.0250.232
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000