Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-06-07 20:28 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4672
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4407
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4434
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4387
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 1100/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3Drop 1.31.0  (landing page)
Tallulah Andrews
Snapshot Date: 2024-06-05 14:00:27 -0400 (Wed, 05 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
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for M3Drop on merida1

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: /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_1.31.0.tar.gz
StartedAt: 2024-06-06 05:26:51 -0400 (Thu, 06 Jun 2024)
EndedAt: 2024-06-06 05:37:11 -0400 (Thu, 06 Jun 2024)
EllapsedTime: 620.8 seconds
RetCode: 0
Status:   OK  
CheckDir: M3Drop.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/M3Drop.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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             157.497  3.437 202.891
Imputation                  56.812  0.837  73.945
M3D_getmarkers              54.796  1.750  70.313
M3D_ConverData               7.371  0.356   9.674
Brennecke_getVariableGenes   4.241  0.429   7.418
* 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
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/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_getVariableGenes4.2410.4297.418
Consensus_FS0.4110.0480.625
Fitting_Dropout_Models0.0000.0000.001
Imputation56.812 0.83773.945
M3D_Clean_Data1.5610.0902.083
M3D_ConverData7.3710.3569.674
M3D_Differential_Expression1.7360.0802.319
M3D_Dropout_Models1.6400.0842.191
M3D_Expression_Heatmap0.6670.0170.842
M3D_Get_Extremes1.6590.1322.262
M3D_Get_Heatmap_Cell_Clusters0.6140.0160.798
M3D_Simulations0.0010.0010.000
M3D_Test_Shift1.1120.0551.447
M3D_ThreeSet_Venn0.4030.0100.502
M3D_TraditionalDE0.0130.0010.017
M3D_getmarkers54.796 1.75070.313
M3D_horz_res0.0000.0010.004
NBumi_CheckFit1.9140.1412.575
NBumi_CoExpression1.7490.0422.172
NBumi_CompareModels3.3140.1834.471
NBumi_ConvertToInteger0.0010.0000.001
NBumi_ConvrtData0.5110.0390.734
NBumi_FSDrop1.9370.0592.462
NBumi_FSHighVar1.0800.0421.434
NBumi_FSOther0.0120.0000.015
NBumi_FitDisp000
NBumi_FitDispVsMean0.9110.0331.177
NBumi_FitModel1.0910.0421.414
NBumi_HVG1.1790.0381.587
NBumi_PearsonResiduals1.2170.0581.708
NBumi_TradDE0.0000.0000.001
NewSimulations157.497 3.437202.891
Other_FS1.3450.0301.693
PoissonUMIFeatureSelectionDropouts1.0970.0531.400
bg__fit_gamma0.0010.0000.000
bg__get_stats000
bg__mean2disp0.0000.0000.001
bg__shift_size0.0000.0000.001
bg__var_vs_drop000