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This page was generated on 2023-04-12 11:06:13 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 lconway


To the developers/maintainers of the M3Drop package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/M3Drop.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1068/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.24.0  (landing page)
Tallulah Andrews
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: RELEASE_3_16
git_last_commit: 4e29540
git_last_commit_date: 2022-11-01 11:14:44 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: M3Drop
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings M3Drop_1.24.0.tar.gz
StartedAt: 2023-04-10 20:57:17 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:02:32 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 314.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: M3Drop.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings M3Drop_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/M3Drop.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.24.0’
* 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 ... 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 112.033  9.908 122.356
Imputation      38.752  0.147  38.986
M3D_getmarkers  28.867  0.641  29.607
* 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
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/M3Drop.Rcheck/00check.log’
for details.



Installation output

M3Drop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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_getVariableGenes2.9060.2033.118
Consensus_FS0.2510.0230.275
Fitting_Dropout_Models0.0000.0000.001
Imputation38.752 0.14738.986
M3D_Clean_Data1.6380.1241.768
M3D_ConverData4.3410.1914.561
M3D_Differential_Expression1.1660.0551.225
M3D_Dropout_Models1.3820.0721.458
M3D_Expression_Heatmap0.5230.0110.537
M3D_Get_Extremes1.4050.1341.544
M3D_Get_Heatmap_Cell_Clusters0.4370.0090.447
M3D_Simulations0.0000.0000.001
M3D_Test_Shift0.4460.0390.487
M3D_ThreeSet_Venn0.3350.0080.344
M3D_TraditionalDE0.0140.0000.014
M3D_getmarkers28.867 0.64129.607
M3D_horz_res000
NBumi_CheckFit1.7770.1321.915
NBumi_CoExpression0.6180.1080.725
NBumi_CompareModels2.2840.1712.463
NBumi_ConvertToInteger0.0010.0000.001
NBumi_ConvrtData0.3430.0140.358
NBumi_FSDrop1.3820.0941.479
NBumi_FSHighVar0.6610.0900.781
NBumi_FSOther0.0130.0010.014
NBumi_FitDisp0.0000.0010.001
NBumi_FitDispVsMean0.4490.0140.465
NBumi_FitModel1.1710.0821.260
NBumi_HVG0.7710.0810.855
NBumi_TradDE0.0000.0010.000
NewSimulations112.033 9.908122.356
Other_FS1.0650.0161.084
PoissonUMIFeatureSelectionDropouts0.5580.0110.571
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size0.0000.0010.000
bg__var_vs_drop000