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This page was generated on 2023-11-02 11:40:52 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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

Package 1122/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.28.0  (landing page)
Tallulah Andrews
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: RELEASE_3_18
git_last_commit: 6201a7c
git_last_commit_date: 2023-10-24 10:53:48 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 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 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for M3Drop on kunpeng2


To the developers/maintainers of the M3Drop package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: M3Drop
Version: 1.28.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings M3Drop_1.28.0.tar.gz
StartedAt: 2023-11-02 11:45:28 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 11:52:42 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 433.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: M3Drop.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings M3Drop_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/M3Drop.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.28.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘M3Drop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Simulation Trifecta
> ### Title: Make Simulated Data from a provided scRNASeq dataset.
> ### Aliases: M3DropSimulationTrifecta NBumiSimulationTrifecta
> ### Keywords: simulations, differential expression, differential variance
> 
> ### ** Examples
> 
> 	library(M3DExampleData)
> 	counts <- NBumiConvertData(Mmus_example_list$data)
[1] "Removing  18 undetected genes."
> 	norm <- M3DropConvertData(Mmus_example_list$data, is.log=FALSE, is.counts=TRUE)
[1] "Removing  18 undetected genes."
> 	ZINB_sim <- M3DropSimulationTrifecta(norm)
> 	DANB_sim <- NBumiSimulationTrifecta(counts)
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/M3Drop.Rcheck/00check.log’
for details.


Installation output

M3Drop.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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_getVariableGenes5.2790.2205.516
Consensus_FS1.9590.0121.974
Fitting_Dropout_Models000
Imputation79.722 0.99882.563
M3D_Clean_Data2.1420.1032.271
M3D_ConverData7.7470.2047.969
M3D_Differential_Expression2.6520.0562.714
M3D_Dropout_Models1.5110.0201.535
M3D_Expression_Heatmap0.4950.0040.501
M3D_Get_Extremes4.1210.0404.167
M3D_Get_Heatmap_Cell_Clusters0.4460.0040.452
M3D_Simulations000
M3D_Test_Shift0.9570.0040.963
M3D_ThreeSet_Venn0.2710.0000.272
M3D_TraditionalDE0.0120.0000.013
M3D_getmarkers47.642 0.24347.988
M3D_horz_res000
NBumi_CheckFit3.4340.0843.526
NBumi_CoExpression2.7120.0242.742
NBumi_CompareModels5.5870.0205.620
NBumi_ConvertToInteger0.0010.0000.000
NBumi_ConvrtData0.4560.0000.458
NBumi_FSDrop2.3130.0402.358
NBumi_FSHighVar1.9300.0561.990
NBumi_FSOther0.0130.0000.014
NBumi_FitDisp000
NBumi_FitDispVsMean1.5320.0321.567
NBumi_FitModel2.7150.0202.741
NBumi_HVG2.1600.0162.181
NBumi_TradDE0.0010.0000.000