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

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### Running command:
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###   /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.

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### Running command:
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###   /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)

name	user	system	elapsed
Brennecke_getVariableGenes	3.056	0.088	3.238
Consensus_FS	0.428	0.000	0.428
Fitting_Dropout_Models	0	0	0
Imputation	92.916	0.044	93.172
M3D_Clean_Data	0.908	0.016	0.934
M3D_ConverData	7.748	0.264	8.059
M3D_Differential_Expression	1.440	0.060	1.506
M3D_Dropout_Models	1.200	0.068	1.273
M3D_Expression_Heatmap	0.344	0.000	0.344
M3D_Get_Extremes	2.056	0.076	2.134
M3D_Get_Heatmap_Cell_Clusters	0.304	0.004	0.307
M3D_Simulations	0	0	0
M3D_Test_Shift	0.668	0.000	0.669
M3D_ThreeSet_Venn	0.080	0.000	0.081
M3D_TraditionalDE	0.020	0.000	0.019
M3D_getmarkers	53.548	0.012	54.349
M3D_horz_res	0	0	0
NBumi_CheckFit	2.068	0.024	2.094
NBumi_CoExpression	1.720	0.008	1.735
NBumi_CompareModels	3.660	0.004	3.776
NBumi_ConvertToInteger	0.000	0.000	0.001
NBumi_ConvrtData	0.884	0.000	0.887
NBumi_FSDrop	2.384	0.004	2.671
NBumi_FSHighVar	0.928	0.024	0.981
NBumi_FSOther	0.008	0.000	0.009
NBumi_FitDisp	0	0	0
NBumi_FitDispVsMean	0.780	0.000	0.781
NBumi_FitModel	1.388	0.020	1.409
NBumi_HVG	1.904	0.008	1.972
NBumi_TradDE	0	0	0
NewSimulations	209.404	1.056	213.428
Other_FS	0.960	0.084	1.064
PoissonUMIFeatureSelectionDropouts	1.180	0.000	1.225
bg__fit_gamma	0	0	0
bg__get_stats	0	0	0
bg__mean2disp	0	0	0
bg__shift_size	0	0	0
bg__var_vs_drop	0.004	0.000	0.001