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This page was generated on 2023-01-02 09:00:36 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the M3Drop package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1052/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.25.0  (landing page)
Tallulah Andrews
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: master
git_last_commit: 8cf1b5d
git_last_commit_date: 2022-11-01 11:14:44 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: M3Drop
Version: 1.25.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:M3Drop.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings M3Drop_1.25.0.tar.gz
StartedAt: 2022-12-29 00:59:07 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 01:04:46 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 338.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: M3Drop.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:M3Drop.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings M3Drop_1.25.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/M3Drop.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'M3Drop/DESCRIPTION' ... OK
* this is package 'M3Drop' version '1.25.0'
* 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 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 111.35   2.21  113.58
Imputation      75.39   0.20   75.60
M3D_getmarkers  28.27   0.46   28.72
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/M3Drop.Rcheck/00check.log'
for details.



Installation output

M3Drop.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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_getVariableGenes2.790.112.99
Consensus_FS0.240.020.25
Fitting_Dropout_Models000
Imputation75.39 0.2075.60
M3D_Clean_Data1.240.051.29
M3D_ConverData3.830.374.21
M3D_Differential_Expression1.140.051.18
M3D_Dropout_Models1.480.061.55
M3D_Expression_Heatmap0.450.020.47
M3D_Get_Extremes1.970.202.17
M3D_Get_Heatmap_Cell_Clusters0.430.000.42
M3D_Simulations000
M3D_Test_Shift0.530.040.58
M3D_ThreeSet_Venn0.320.000.32
M3D_TraditionalDE000
M3D_getmarkers28.27 0.4628.72
M3D_horz_res000
NBumi_CheckFit1.930.062.00
NBumi_CoExpression1.110.031.14
NBumi_CompareModels2.610.062.67
NBumi_ConvertToInteger000
NBumi_ConvrtData0.270.000.26
NBumi_FSDrop1.000.021.02
NBumi_FSHighVar0.580.030.61
NBumi_FSOther0.020.000.02
NBumi_FitDisp000
NBumi_FitDispVsMean0.420.010.44
NBumi_FitModel1.110.021.12
NBumi_HVG0.800.060.86
NBumi_TradDE000
NewSimulations111.35 2.21113.58
Other_FS1.490.071.56
PoissonUMIFeatureSelectionDropouts0.590.020.61
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000