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This page was generated on 2024-04-29 11:38:18 -0400 (Mon, 29 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4752
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4518
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4475
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 1136/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.29.7  (landing page)
Tallulah Andrews
Snapshot Date: 2024-04-28 14:00:16 -0400 (Sun, 28 Apr 2024)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: devel
git_last_commit: cced8b7
git_last_commit_date: 2024-03-25 18:22:33 -0400 (Mon, 25 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for M3Drop on palomino3


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.

raw results


Summary

Package: M3Drop
Version: 1.29.7
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:M3Drop.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings M3Drop_1.29.7.tar.gz
StartedAt: 2024-04-29 03:21:07 -0400 (Mon, 29 Apr 2024)
EndedAt: 2024-04-29 03:27:44 -0400 (Mon, 29 Apr 2024)
EllapsedTime: 397.2 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:M3Drop.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings M3Drop_1.29.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/M3Drop.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'M3Drop/DESCRIPTION' ... OK
* this is package 'M3Drop' version '1.29.7'
* 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 code 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
Namespace in Imports field not imported from: 'scater'
  All declared Imports should be used.
* 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 116.90   2.44  119.35
Imputation      75.98   0.64   76.64
M3D_getmarkers  37.61   1.34   38.95
M3D_ConverData   5.86   0.44    6.29
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/M3Drop.Rcheck/00check.log'
for details.


Installation output

M3Drop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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_getVariableGenes4.100.194.42
Consensus_FS0.390.030.42
Fitting_Dropout_Models000
Imputation75.98 0.6476.64
M3D_Clean_Data1.860.172.03
M3D_ConverData5.860.446.29
M3D_Differential_Expression1.780.151.94
M3D_Dropout_Models1.870.111.98
M3D_Expression_Heatmap0.520.020.53
M3D_Get_Extremes2.800.333.14
M3D_Get_Heatmap_Cell_Clusters0.430.010.46
M3D_Simulations000
M3D_Test_Shift0.740.050.78
M3D_ThreeSet_Venn0.330.000.33
M3D_TraditionalDE0.010.000.01
M3D_getmarkers37.61 1.3438.95
M3D_horz_res000
NBumi_CheckFit2.090.212.38
NBumi_CoExpression1.550.171.72
NBumi_CompareModels3.050.373.42
NBumi_ConvertToInteger000
NBumi_ConvrtData0.340.030.38
NBumi_FSDrop1.770.161.92
NBumi_FSHighVar0.680.160.83
NBumi_FSOther0.010.000.02
NBumi_FitDisp000
NBumi_FitDispVsMean0.660.060.72
NBumi_FitModel0.730.120.85
NBumi_HVG1.530.161.69
NBumi_PearsonResiduals1.390.251.64
NBumi_TradDE000
NewSimulations116.90 2.44119.35
Other_FS0.980.051.03
PoissonUMIFeatureSelectionDropouts0.670.200.88
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000