Tallulah Andrews
| Snapshot Date: 2022-01-03 13:55:13 -0500 (Mon, 03 Jan 2022) |
| git_url: https://git.bioconductor.org/packages/M3Drop |
| git_branch: master |
| git_last_commit: be2d07b |
| git_last_commit_date: 2021-10-26 12:31:05 -0500 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-01-04 11:06:18 -0500 (Tue, 04 Jan 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2021-11-10 r81171) -- "Unsuffered Consequences" | 4307 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4044 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences" | 4122 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1019/2072 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| M3Drop 1.21.0 (landing page) Tallulah Andrews
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: M3Drop |
| Version: 1.21.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:M3Drop.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings M3Drop_1.21.0.tar.gz |
| StartedAt: 2022-01-03 19:19:30 -0500 (Mon, 03 Jan 2022) |
| EndedAt: 2022-01-03 19:25:12 -0500 (Mon, 03 Jan 2022) |
| EllapsedTime: 341.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: M3Drop.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:M3Drop.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings M3Drop_1.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/M3Drop.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'M3Drop/DESCRIPTION' ... OK
* this is package 'M3Drop' version '1.21.0'
* 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 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NewSimulations 129.42 5.42 134.84
Imputation 61.94 0.17 62.11
M3D_getmarkers 30.40 0.19 30.59
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/M3Drop.Rcheck/00check.log'
for details.
M3Drop.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL M3Drop
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'M3Drop' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'M3Drop'
finding HTML links ... done
Brennecke_getVariableGenes html
Consensus_FS html
Fitting_Dropout_Models html
Imputation html
M3D_Clean_Data html
M3D_ConverData html
M3D_Differential_Expression html
M3D_Dropout_Models html
M3D_Expression_Heatmap html
M3D_Get_Extremes html
M3D_Get_Heatmap_Cell_Clusters html
M3D_Plotting html
M3D_Simulations html
M3D_Test_Shift html
M3D_ThreeSet_Venn html
M3D_TraditionalDE html
M3D_calc_var html
M3D_getmarkers html
M3D_horz_res html
NBumi_CheckFit html
NBumi_CoExpression html
NBumi_CompareModels html
NBumi_ConvertToInteger html
NBumi_ConvrtData html
NBumi_FSDrop html
NBumi_FSHighVar html
NBumi_FSOther html
NBumi_FitDisp html
NBumi_FitDispVsMean html
NBumi_FitModel html
NBumi_HVG html
NBumi_TradDE html
NewSimulations html
Other_FS html
PoissonUMIFeatureSelectionDropouts html
bg__fit_gamma html
bg__get_stats html
bg__mean2disp html
bg__shift_size html
bg__var_vs_drop html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'GSAR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RCy3' is missing or broken
done
M3Drop.Rcheck/M3Drop-Ex.timings
| name | user | system | elapsed | |
| Brennecke_getVariableGenes | 3.03 | 0.36 | 3.39 | |
| Consensus_FS | 0.27 | 0.02 | 0.28 | |
| Fitting_Dropout_Models | 0 | 0 | 0 | |
| Imputation | 61.94 | 0.17 | 62.11 | |
| M3D_Clean_Data | 1.33 | 0.30 | 1.63 | |
| M3D_ConverData | 3.82 | 0.34 | 4.17 | |
| M3D_Differential_Expression | 0.66 | 0.19 | 0.84 | |
| M3D_Dropout_Models | 1.92 | 0.17 | 2.09 | |
| M3D_Expression_Heatmap | 0.40 | 0.02 | 0.42 | |
| M3D_Get_Extremes | 2.08 | 0.45 | 2.54 | |
| M3D_Get_Heatmap_Cell_Clusters | 0.39 | 0.00 | 0.39 | |
| M3D_Simulations | 0 | 0 | 0 | |
| M3D_Test_Shift | 0.61 | 0.12 | 0.73 | |
| M3D_ThreeSet_Venn | 0.33 | 0.02 | 0.34 | |
| M3D_TraditionalDE | 0.02 | 0.00 | 0.02 | |
| M3D_getmarkers | 30.40 | 0.19 | 30.59 | |
| M3D_horz_res | 0 | 0 | 0 | |
| NBumi_CheckFit | 2.35 | 0.19 | 2.53 | |
| NBumi_CoExpression | 1.34 | 0.09 | 1.44 | |
| NBumi_CompareModels | 3.06 | 0.38 | 3.44 | |
| NBumi_ConvertToInteger | 0 | 0 | 0 | |
| NBumi_ConvrtData | 0.33 | 0.03 | 0.35 | |
| NBumi_FSDrop | 1.34 | 0.20 | 1.55 | |
| NBumi_FSHighVar | 0.91 | 0.16 | 1.06 | |
| NBumi_FSOther | 0.02 | 0.00 | 0.02 | |
| NBumi_FitDisp | 0 | 0 | 0 | |
| NBumi_FitDispVsMean | 0.61 | 0.03 | 0.64 | |
| NBumi_FitModel | 1.89 | 0.13 | 2.01 | |
| NBumi_HVG | 0.71 | 0.20 | 0.91 | |
| NBumi_TradDE | 0 | 0 | 0 | |
| NewSimulations | 129.42 | 5.42 | 134.84 | |
| Other_FS | 1.12 | 0.02 | 1.14 | |
| PoissonUMIFeatureSelectionDropouts | 0.67 | 0.08 | 0.75 | |
| bg__fit_gamma | 0 | 0 | 0 | |
| bg__get_stats | 0 | 0 | 0 | |
| bg__mean2disp | 0 | 0 | 0 | |
| bg__shift_size | 0 | 0 | 0 | |
| bg__var_vs_drop | 0 | 0 | 0 | |