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This page was generated on 2024-06-14 12:02 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1104/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.31.0  (landing page)
Tallulah Andrews
Snapshot Date: 2024-06-13 14:00 -0400 (Thu, 13 Jun 2024)
git_url: https://git.bioconductor.org/packages/M3Drop
git_branch: devel
git_last_commit: 65bab9c
git_last_commit_date: 2024-04-30 10:54:44 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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


CHECK results for M3Drop on nebbiolo2

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: 1.31.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings M3Drop_1.31.0.tar.gz
StartedAt: 2024-06-14 00:58:43 -0400 (Fri, 14 Jun 2024)
EndedAt: 2024-06-14 01:05:27 -0400 (Fri, 14 Jun 2024)
EllapsedTime: 404.8 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings M3Drop_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/M3Drop.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.31.0’
* 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 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
NewSimulations 98.643  1.540 100.185
Imputation     39.608  0.131  39.740
M3D_getmarkers 32.910  0.296  33.207
M3D_ConverData  5.486  0.164   5.650
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/M3Drop.Rcheck/00check.log’
for details.


Installation output

M3Drop.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL M3Drop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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_getVariableGenes3.5300.1793.710
Consensus_FS0.2500.0040.254
Fitting_Dropout_Models000
Imputation39.608 0.13139.740
M3D_Clean_Data1.8940.1112.006
M3D_ConverData5.4860.1645.650
M3D_Differential_Expression2.2420.1162.358
M3D_Dropout_Models1.7640.0911.872
M3D_Expression_Heatmap0.4800.0040.484
M3D_Get_Extremes1.6610.0681.739
M3D_Get_Heatmap_Cell_Clusters0.4220.0080.430
M3D_Simulations0.0000.0010.000
M3D_Test_Shift1.2820.0101.293
M3D_ThreeSet_Venn0.3160.0080.323
M3D_TraditionalDE0.0120.0000.011
M3D_getmarkers32.910 0.29633.207
M3D_horz_res000
NBumi_CheckFit1.4200.0681.489
NBumi_CoExpression1.4720.0801.551
NBumi_CompareModels2.8380.0842.923
NBumi_ConvertToInteger0.0010.0000.000
NBumi_ConvrtData0.3320.0000.331
NBumi_FSDrop1.5420.0361.578
NBumi_FSHighVar0.7030.0280.730
NBumi_FSOther0.0090.0000.009
NBumi_FitDisp000
NBumi_FitDispVsMean0.4950.0000.494
NBumi_FitModel0.6920.0600.753
NBumi_HVG1.4290.0761.506
NBumi_PearsonResiduals0.7310.0320.762
NBumi_TradDE0.0000.0000.001
NewSimulations 98.643 1.540100.185
Other_FS1.0400.0081.047
PoissonUMIFeatureSelectionDropouts0.5870.0080.594
bg__fit_gamma000
bg__get_stats000
bg__mean2disp000
bg__shift_size000
bg__var_vs_drop000