Tallulah Andrews
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/M3Drop |
| Branch: master |
| Last Commit: 6d00bdd |
| Last Changed Date: 2019-01-04 13:37:11 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:17:10 -0400 (Tue, 09 Apr 2019).
| Package 883/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| M3Drop 1.9.4 Tallulah Andrews
| malbec2 | Linux (Ubuntu 18.04.2 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: M3Drop |
| Version: 1.9.4 |
| 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_1.9.4.tar.gz |
| StartedAt: 2019-04-09 03:09:11 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:19:31 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 619.7 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_1.9.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3Drop.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.4’
* 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
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:
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 257.118 52.167 310.649
Imputation 74.559 0.317 74.878
M3D_getmarkers 65.203 1.776 66.980
M3D_ConverData 10.133 0.844 11.033
NBumi_CompareModels 4.917 0.543 5.683
* 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-3.9-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 | 4.030 | 0.456 | 4.493 | |
| Consensus_FS | 0.406 | 0.044 | 0.451 | |
| Fitting_Dropout_Models | 0.001 | 0.000 | 0.000 | |
| Imputation | 74.559 | 0.317 | 74.878 | |
| M3D_Clean_Data | 1.517 | 0.295 | 1.811 | |
| M3D_ConverData | 10.133 | 0.844 | 11.033 | |
| M3D_Differential_Expression | 1.636 | 0.283 | 1.919 | |
| M3D_Dropout_Models | 1.450 | 0.270 | 1.722 | |
| M3D_Expression_Heatmap | 0.440 | 0.012 | 0.453 | |
| M3D_Get_Extremes | 1.600 | 0.510 | 2.113 | |
| M3D_Get_Heatmap_Cell_Clusters | 0.386 | 0.007 | 0.394 | |
| M3D_Simulations | 0.000 | 0.000 | 0.001 | |
| M3D_Test_Shift | 1.241 | 0.151 | 1.393 | |
| M3D_ThreeSet_Venn | 0.063 | 0.004 | 0.070 | |
| M3D_TraditionalDE | 0.021 | 0.001 | 0.022 | |
| M3D_getmarkers | 65.203 | 1.776 | 66.980 | |
| M3D_horz_res | 0 | 0 | 0 | |
| NBumi_CheckFit | 3.176 | 0.380 | 3.624 | |
| NBumi_CompareModels | 4.917 | 0.543 | 5.683 | |
| NBumi_ConvertToInteger | 0.001 | 0.000 | 0.001 | |
| NBumi_ConvrtData | 1.226 | 0.023 | 1.300 | |
| NBumi_FSDrop | 3.029 | 0.304 | 3.477 | |
| NBumi_FSHighVar | 1.920 | 0.371 | 2.400 | |
| NBumi_FSOther | 0.025 | 0.001 | 0.027 | |
| NBumi_FitDisp | 0.000 | 0.001 | 0.000 | |
| NBumi_FitDispVsMean | 1.588 | 0.077 | 1.744 | |
| NBumi_FitModel | 1.993 | 0.270 | 2.338 | |
| NBumi_TradDE | 0 | 0 | 0 | |
| NewSimulations | 257.118 | 52.167 | 310.649 | |
| Other_FS | 0.341 | 0.026 | 0.367 | |
| PoissonUMIFeatureSelectionDropouts | 1.641 | 0.280 | 1.922 | |
| 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 | 0.000 | 0.000 | 0.001 | |