Tallulah Andrews
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/M3Drop |
| Branch: master |
| Last Commit: a91f5d3 |
| Last Changed Date: 2019-10-29 13:42:09 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:46:32 -0500 (Thu, 16 Jan 2020).
| Package 930/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| M3Drop 1.13.0 Tallulah Andrews
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: M3Drop |
| Version: 1.13.0 |
| 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_1.13.0.tar.gz |
| StartedAt: 2020-01-16 05:59:19 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 06:11:01 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 701.7 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_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/M3Drop.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.13.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
NewSimulations 291.828 51.194 343.390
M3D_getmarkers 77.810 1.612 81.784
Imputation 78.798 0.448 79.255
M3D_ConverData 10.800 0.787 11.629
* 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-3.11-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/4.0/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 | 4.338 | 0.535 | 4.885 | |
| Consensus_FS | 0.947 | 0.126 | 1.074 | |
| Fitting_Dropout_Models | 0 | 0 | 0 | |
| Imputation | 78.798 | 0.448 | 79.255 | |
| M3D_Clean_Data | 1.307 | 0.261 | 1.568 | |
| M3D_ConverData | 10.800 | 0.787 | 11.629 | |
| M3D_Differential_Expression | 0.890 | 0.260 | 1.152 | |
| M3D_Dropout_Models | 1.586 | 0.283 | 1.874 | |
| M3D_Expression_Heatmap | 0.453 | 0.016 | 0.477 | |
| M3D_Get_Extremes | 2.560 | 0.561 | 3.126 | |
| M3D_Get_Heatmap_Cell_Clusters | 0.329 | 0.014 | 0.348 | |
| M3D_Simulations | 0.000 | 0.000 | 0.001 | |
| M3D_Test_Shift | 0.665 | 0.164 | 0.835 | |
| M3D_ThreeSet_Venn | 0.083 | 0.006 | 0.092 | |
| M3D_TraditionalDE | 0.030 | 0.001 | 0.031 | |
| M3D_getmarkers | 77.810 | 1.612 | 81.784 | |
| M3D_horz_res | 0.001 | 0.000 | 0.001 | |
| NBumi_CheckFit | 3.123 | 0.373 | 3.519 | |
| NBumi_CoExpression | 2.658 | 0.301 | 2.959 | |
| NBumi_CompareModels | 3.985 | 0.540 | 4.527 | |
| NBumi_ConvertToInteger | 0.001 | 0.001 | 0.001 | |
| NBumi_ConvrtData | 1.142 | 0.055 | 1.197 | |
| NBumi_FSDrop | 3.112 | 0.420 | 3.532 | |
| NBumi_FSHighVar | 1.472 | 0.302 | 1.775 | |
| NBumi_FSOther | 0.021 | 0.000 | 0.021 | |
| NBumi_FitDisp | 0.000 | 0.000 | 0.001 | |
| NBumi_FitDispVsMean | 1.509 | 0.096 | 1.604 | |
| NBumi_FitModel | 2.342 | 0.196 | 2.539 | |
| NBumi_HVG | 2.121 | 0.526 | 2.647 | |
| NBumi_TradDE | 0.000 | 0.000 | 0.001 | |
| NewSimulations | 291.828 | 51.194 | 343.390 | |
| Other_FS | 0.401 | 0.029 | 0.468 | |
| PoissonUMIFeatureSelectionDropouts | 2.137 | 0.321 | 2.459 | |
| bg__fit_gamma | 0 | 0 | 0 | |
| bg__get_stats | 0.000 | 0.001 | 0.001 | |
| bg__mean2disp | 0 | 0 | 0 | |
| bg__shift_size | 0.000 | 0.000 | 0.001 | |
| bg__var_vs_drop | 0.000 | 0.000 | 0.001 | |