Multiple platform build/check report for BioC 3.9 - CHECK report for M3Drop on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings M3Drop_1.9.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/M3Drop.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.4’
* 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
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:
  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 181.167  1.207 182.707
Imputation      85.997  0.016  86.040
M3D_getmarkers  54.213  0.004  54.525
M3D_ConverData   5.532  0.282   6.175
* 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-3.9-bioc/meat/M3Drop.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL M3Drop
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* installing to library ‘/home/biocbuild/bbs-3.9-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

name	user	system	elapsed
Brennecke_getVariableGenes	2.548	0.060	2.713
Consensus_FS	0.452	0.000	0.452
Fitting_Dropout_Models	0	0	0
Imputation	85.997	0.016	86.040
M3D_Clean_Data	1.287	0.071	1.359
M3D_ConverData	5.532	0.282	6.175
M3D_Differential_Expression	1.460	0.056	1.516
M3D_Dropout_Models	1.460	0.063	1.524
M3D_Expression_Heatmap	0.379	0.004	0.383
M3D_Get_Extremes	1.551	0.019	1.571
M3D_Get_Heatmap_Cell_Clusters	0.249	0.000	0.249
M3D_Simulations	0	0	0
M3D_Test_Shift	1.138	0.007	1.147
M3D_ThreeSet_Venn	0.071	0.000	0.072
M3D_TraditionalDE	0.011	0.004	0.015
M3D_getmarkers	54.213	0.004	54.525
M3D_horz_res	0	0	0
NBumi_CheckFit	2.160	0.031	2.193
NBumi_CompareModels	3.457	0.028	3.494
NBumi_ConvertToInteger	0.000	0.000	0.001
NBumi_ConvrtData	0.797	0.004	0.807
NBumi_FSDrop	1.349	0.000	1.352
NBumi_FSHighVar	1.108	0.000	1.119
NBumi_FSOther	0.015	0.000	0.015
NBumi_FitDisp	0	0	0
NBumi_FitDispVsMean	0.842	0.004	0.846
NBumi_FitModel	1.691	0.007	1.717
NBumi_TradDE	0	0	0
NewSimulations	181.167	1.207	182.707
Other_FS	0.302	0.000	0.302
PoissonUMIFeatureSelectionDropouts	0.931	0.000	0.931
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	0.000	0.000	0.001

CHECK report for M3Drop on malbec2

Summary

Command output

Installation output

Tests output

Example timings