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CHECK report for M3Drop on malbec1

This page was generated on 2020-04-15 12:12:01 -0400 (Wed, 15 Apr 2020).

Package 933/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.12.0
Tallulah Andrews
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/M3Drop
Branch: RELEASE_3_10
Last Commit: 5552690
Last Changed Date: 2019-10-29 13:10:13 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: M3Drop
Version: 1.12.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings M3Drop_1.12.0.tar.gz
StartedAt: 2020-04-15 04:18:22 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:26:35 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 492.9 seconds
RetCode: 0
Status:  OK 
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings M3Drop_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/M3Drop.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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 or elapsed time > 5s
                  user system elapsed
NewSimulations 209.404  1.056 213.428
Imputation      92.916  0.044  93.172
M3D_getmarkers  53.548  0.012  54.349
M3D_ConverData   7.748  0.264   8.059
* 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-3.10-bioc/meat/M3Drop.Rcheck/00check.log’
for details.



Installation output

M3Drop.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL M3Drop
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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_getVariableGenes3.0560.0883.238
Consensus_FS0.4280.0000.428
Fitting_Dropout_Models000
Imputation92.916 0.04493.172
M3D_Clean_Data0.9080.0160.934
M3D_ConverData7.7480.2648.059
M3D_Differential_Expression1.4400.0601.506
M3D_Dropout_Models1.2000.0681.273
M3D_Expression_Heatmap0.3440.0000.344
M3D_Get_Extremes2.0560.0762.134
M3D_Get_Heatmap_Cell_Clusters0.3040.0040.307
M3D_Simulations000
M3D_Test_Shift0.6680.0000.669
M3D_ThreeSet_Venn0.0800.0000.081
M3D_TraditionalDE0.0200.0000.019
M3D_getmarkers53.548 0.01254.349
M3D_horz_res000
NBumi_CheckFit2.0680.0242.094
NBumi_CoExpression1.7200.0081.735
NBumi_CompareModels3.6600.0043.776
NBumi_ConvertToInteger0.0000.0000.001
NBumi_ConvrtData0.8840.0000.887
NBumi_FSDrop2.3840.0042.671
NBumi_FSHighVar0.9280.0240.981
NBumi_FSOther0.0080.0000.009
NBumi_FitDisp000
NBumi_FitDispVsMean0.7800.0000.781
NBumi_FitModel1.3880.0201.409
NBumi_HVG1.9040.0081.972
NBumi_TradDE000
NewSimulations209.404 1.056213.428
Other_FS0.9600.0841.064
PoissonUMIFeatureSelectionDropouts1.1800.0001.225
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop0.0040.0000.001