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CHECK report for M3Drop on malbec1

This page was generated on 2021-05-06 12:28:06 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the M3Drop package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 981/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.16.0  (landing page)
Tallulah Andrews
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/M3Drop
Branch: RELEASE_3_12
Last Commit: 17f0450
Last Changed Date: 2020-10-27 11:19:00 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: M3Drop
Version: 1.16.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings M3Drop_1.16.0.tar.gz
StartedAt: 2021-05-06 03:00:35 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:08:39 -0400 (Thu, 06 May 2021)
EllapsedTime: 484.2 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings M3Drop_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/M3Drop.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.16.0’
* 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 ... NOTE
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
NewSimulations             203.092  0.816 204.386
Imputation                  84.356  0.032  84.570
M3D_getmarkers              55.296  0.136  55.578
M3D_ConverData               8.124  0.120   8.832
Brennecke_getVariableGenes   5.368  0.112   5.568
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/M3Drop.Rcheck/00check.log’
for details.



Installation output

M3Drop.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL M3Drop
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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_getVariableGenes5.3680.1125.568
Consensus_FS0.4720.0040.475
Fitting_Dropout_Models000
Imputation84.356 0.03284.570
M3D_Clean_Data1.6440.0321.681
M3D_ConverData8.1240.1208.832
M3D_Differential_Expression2.4080.0802.488
M3D_Dropout_Models1.5000.0601.568
M3D_Expression_Heatmap0.6920.0080.704
M3D_Get_Extremes3.1240.0323.164
M3D_Get_Heatmap_Cell_Clusters0.5800.0040.588
M3D_Simulations000
M3D_Test_Shift0.8840.0080.894
M3D_ThreeSet_Venn0.3880.0040.395
M3D_TraditionalDE0.0080.0000.011
M3D_getmarkers55.296 0.13655.578
M3D_horz_res0.0040.0000.000
NBumi_CheckFit2.4360.0642.501
NBumi_CoExpression1.1880.0321.221
NBumi_CompareModels4.8680.0444.914
NBumi_ConvertToInteger0.0000.0000.001
NBumi_ConvrtData0.9560.0000.958
NBumi_FSDrop1.3720.0121.387
NBumi_FSHighVar1.2120.0121.224
NBumi_FSOther0.0160.0000.017
NBumi_FitDisp000
NBumi_FitDispVsMean0.8960.0000.897
NBumi_FitModel1.4680.0121.480
NBumi_HVG0.9520.0160.968
NBumi_TradDE000
NewSimulations203.092 0.816204.386
Other_FS1.0280.0081.036
PoissonUMIFeatureSelectionDropouts0.7600.0000.763
bg__fit_gamma000
bg__get_stats0.0000.0000.001
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000