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This page was generated on 2022-10-19 13:23:11 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for M3Drop on merida1


To the developers/maintainers of the M3Drop package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1049/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.22.0  (landing page)
Tallulah Andrews
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: RELEASE_3_15
git_last_commit: 251aea9
git_last_commit_date: 2022-04-26 11:37:02 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: M3Drop
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2022-10-19 04:05:35 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 04:17:30 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 715.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: M3Drop.Rcheck
Warnings: 1

Command output

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### 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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/M3Drop.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.22.0’
* 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 R 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 ... WARNING
Package in Depends field not imported from: ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘scater::exprs’
* 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             306.435 12.785 319.767
Imputation                  84.109  0.185  84.421
M3D_getmarkers              72.824  0.805  73.757
M3D_ConverData               9.569  0.259   9.843
Brennecke_getVariableGenes   5.679  0.267   5.958
NBumi_CompareModels          5.522  0.158   5.697
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/M3Drop.Rcheck/00check.log’
for details.



Installation output

M3Drop.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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)

Tests output


Example timings

M3Drop.Rcheck/M3Drop-Ex.timings

nameusersystemelapsed
Brennecke_getVariableGenes5.6790.2675.958
Consensus_FS0.5940.0380.634
Fitting_Dropout_Models000
Imputation84.109 0.18584.421
M3D_Clean_Data2.2350.1442.384
M3D_ConverData9.5690.2599.843
M3D_Differential_Expression1.6880.0681.758
M3D_Dropout_Models2.0820.0672.152
M3D_Expression_Heatmap0.8400.0130.855
M3D_Get_Extremes2.2810.1202.406
M3D_Get_Heatmap_Cell_Clusters0.7680.0100.782
M3D_Simulations000
M3D_Test_Shift0.8330.0390.872
M3D_ThreeSet_Venn0.4430.0090.455
M3D_TraditionalDE0.0200.0000.021
M3D_getmarkers72.824 0.80573.757
M3D_horz_res000
NBumi_CheckFit2.7640.0882.860
NBumi_CoExpression2.3950.0732.472
NBumi_CompareModels5.5220.1585.697
NBumi_ConvertToInteger0.0010.0010.001
NBumi_ConvrtData0.6660.0160.682
NBumi_FSDrop2.1830.0422.228
NBumi_FSHighVar1.7200.0371.760
NBumi_FSOther0.0200.0010.020
NBumi_FitDisp000
NBumi_FitDispVsMean1.4430.0211.466
NBumi_FitModel2.2990.0592.360
NBumi_HVG1.8270.0551.885
NBumi_TradDE0.0000.0000.001
NewSimulations306.435 12.785319.767
Other_FS2.3570.2522.616
PoissonUMIFeatureSelectionDropouts1.6990.0161.716
bg__fit_gamma0.0000.0000.001
bg__get_stats0.0010.0000.000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000