Tallulah Andrews
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/M3Drop |
| Branch: RELEASE_3_10 |
| Last Commit: 5552690 |
| Last Changed Date: 2019-10-29 13:10:13 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:44:28 -0400 (Wed, 15 Apr 2020).
| Package 933/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| M3Drop 1.12.0 Tallulah Andrews
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: M3Drop |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3Drop_1.12.0.tar.gz |
| StartedAt: 2020-04-15 03:29:48 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:38:22 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 514.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: M3Drop.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3Drop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3Drop_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/M3Drop.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3Drop/DESCRIPTION’ ... OK
* this is package ‘M3Drop’ version ‘1.12.0’
* 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 dependencies in R code ... NOTE
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
NewSimulations 215.624 18.618 236.148
Imputation 77.507 0.249 78.636
M3D_getmarkers 55.183 0.985 57.015
M3D_ConverData 9.208 0.295 9.777
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/M3Drop.Rcheck/00check.log’
for details.
M3Drop.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL M3Drop ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
M3Drop.Rcheck/M3Drop-Ex.timings
| name | user | system | elapsed | |
| Brennecke_getVariableGenes | 3.260 | 0.245 | 3.625 | |
| Consensus_FS | 0.622 | 0.040 | 0.667 | |
| Fitting_Dropout_Models | 0 | 0 | 0 | |
| Imputation | 77.507 | 0.249 | 78.636 | |
| M3D_Clean_Data | 1.081 | 0.177 | 1.302 | |
| M3D_ConverData | 9.208 | 0.295 | 9.777 | |
| M3D_Differential_Expression | 1.360 | 0.136 | 1.528 | |
| M3D_Dropout_Models | 1.427 | 0.165 | 1.597 | |
| M3D_Expression_Heatmap | 0.406 | 0.008 | 0.443 | |
| M3D_Get_Extremes | 2.155 | 0.312 | 2.522 | |
| M3D_Get_Heatmap_Cell_Clusters | 0.332 | 0.006 | 0.340 | |
| M3D_Simulations | 0 | 0 | 0 | |
| M3D_Test_Shift | 0.666 | 0.086 | 0.753 | |
| M3D_ThreeSet_Venn | 0.076 | 0.004 | 0.081 | |
| M3D_TraditionalDE | 0.012 | 0.001 | 0.012 | |
| M3D_getmarkers | 55.183 | 0.985 | 57.015 | |
| M3D_horz_res | 0.001 | 0.000 | 0.000 | |
| NBumi_CheckFit | 2.204 | 0.175 | 2.401 | |
| NBumi_CoExpression | 1.838 | 0.150 | 1.999 | |
| NBumi_CompareModels | 3.570 | 0.186 | 3.774 | |
| NBumi_ConvertToInteger | 0.001 | 0.000 | 0.001 | |
| NBumi_ConvrtData | 0.703 | 0.012 | 0.719 | |
| NBumi_FSDrop | 2.208 | 0.119 | 2.347 | |
| NBumi_FSHighVar | 1.162 | 0.118 | 1.286 | |
| NBumi_FSOther | 0.007 | 0.000 | 0.008 | |
| NBumi_FitDisp | 0.001 | 0.000 | 0.001 | |
| NBumi_FitDispVsMean | 0.912 | 0.023 | 0.944 | |
| NBumi_FitModel | 1.686 | 0.095 | 1.790 | |
| NBumi_HVG | 1.852 | 0.175 | 2.041 | |
| NBumi_TradDE | 0 | 0 | 0 | |
| NewSimulations | 215.624 | 18.618 | 236.148 | |
| Other_FS | 0.293 | 0.015 | 0.311 | |
| PoissonUMIFeatureSelectionDropouts | 1.293 | 0.091 | 1.401 | |
| bg__fit_gamma | 0.000 | 0.001 | 0.001 | |
| bg__get_stats | 0 | 0 | 0 | |
| bg__mean2disp | 0 | 0 | 0 | |
| bg__shift_size | 0.001 | 0.000 | 0.001 | |
| bg__var_vs_drop | 0 | 0 | 0 | |