Michael Cole
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/scone |
| Branch: RELEASE_3_9 |
| Last Commit: 4d72c47 |
| Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:59:21 -0400 (Wed, 16 Oct 2019).
| Package 1473/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scone 1.8.0 Michael Cole
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: scone |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scone_1.8.0.tar.gz |
| StartedAt: 2019-10-16 06:38:46 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:52:42 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 835.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scone.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scone.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scone_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scone.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scone/DESCRIPTION’ ... OK * this is package ‘scone’ version ‘1.8.0’ * 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 ‘scone’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE sconeReport: no visible global function definition for ‘visNetworkOutput’ sconeReport: no visible global function definition for ‘plotlyOutput’ sconeReport : server: no visible global function definition for ‘renderVisNetwork’ sconeReport : server: no visible global function definition for ‘%>%’ sconeReport : server: no visible global function definition for ‘visNetwork’ sconeReport : server: no visible global function definition for ‘visHierarchicalLayout’ sconeReport : server: no visible global function definition for ‘visGroups’ sconeReport : server: no visible global function definition for ‘visEdges’ sconeReport : server: no visible global function definition for ‘visOptions’ sconeReport : server: no visible global function definition for ‘visLegend’ sconeReport : server: no visible global function definition for ‘visNetworkProxy’ sconeReport : server: no visible global function definition for ‘visSelectNodes’ sconeReport : server: no visible global function definition for ‘plot_ly’ sconeReport : server: no visible global function definition for ‘ggplot’ sconeReport : server: no visible global function definition for ‘aes’ sconeReport : server: no visible global function definition for ‘geom_bar’ sconeReport : server: no visible global function definition for ‘ylim’ sconeReport : server: no visible global function definition for ‘labs’ sconeReport : server: no visible global function definition for ‘theme’ sconeReport : server: no visible global function definition for ‘element_blank’ sconeReport : server: no visible global function definition for ‘ggplotly’ sconeReport : server: no visible global function definition for ‘geom_violin’ sconeReport : server: no visible global function definition for ‘coord_cartesian’ sconeReport : server: no visible global function definition for ‘scale_fill_manual’ sconeReport : server: no visible global function definition for ‘geom_point’ sconeReport : server: no visible global function definition for ‘guides’ Undefined global functions or variables: %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork scale_fill_manual theme visEdges visGroups visHierarchicalLayout visLegend visNetwork visNetworkOutput visNetworkProxy visOptions visSelectNodes ylim * checking Rd files ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/scone.Rcheck/00check.log’ for details.
scone.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scone ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘scone’ ... ** using staged installation ** R ** data ** 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 (scone)
scone.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS" = "")
>
> library(testthat)
> library(scone)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("scone")
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:05)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:05)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:06)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:3 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:39)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:36 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 62 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
191.286 14.744 301.526
scone.Rcheck/scone-Ex.timings
| name | user | system | elapsed | |
| CLR_FN | 0.003 | 0.001 | 0.003 | |
| DESEQ_FN | 0.002 | 0.001 | 0.003 | |
| FQ_FN | 0.004 | 0.001 | 0.005 | |
| SCRAN_FN | 3.234 | 0.134 | 3.369 | |
| SUM_FN | 0.001 | 0.000 | 0.001 | |
| SconeExperiment-class | 0.431 | 0.004 | 0.436 | |
| TMM_FN | 0.005 | 0.001 | 0.007 | |
| UQ_FN | 0.002 | 0.000 | 0.002 | |
| biplot_color | 0.016 | 0.002 | 0.018 | |
| biplot_interactive | 0.382 | 0.017 | 0.399 | |
| control_genes | 0.030 | 0.044 | 0.074 | |
| estimate_ziber | 0.085 | 0.001 | 0.087 | |
| factor_sample_filter | 0.092 | 0.011 | 0.104 | |
| fast_estimate_ziber | 0.061 | 0.005 | 0.066 | |
| get_bio | 0.086 | 0.004 | 0.091 | |
| get_design | 1.066 | 0.186 | 1.251 | |
| get_negconruv | 0.174 | 0.004 | 0.177 | |
| get_normalized | 0.102 | 0.001 | 0.104 | |
| get_params | 0.049 | 0.000 | 0.050 | |
| get_qc | 0.084 | 0.002 | 0.085 | |
| get_scores | 0.054 | 0.001 | 0.055 | |
| impute_expectation | 0.002 | 0.000 | 0.002 | |
| impute_null | 0 | 0 | 0 | |
| lm_adjust | 0.004 | 0.000 | 0.005 | |
| make_design | 0.002 | 0.000 | 0.002 | |
| metric_sample_filter | 0.010 | 0.002 | 0.013 | |
| scone | 0.224 | 0.004 | 0.229 | |
| sconeReport | 0.113 | 0.002 | 0.115 | |
| scone_easybake | 0.112 | 0.001 | 0.113 | |
| score_matrix | 0.008 | 0.000 | 0.009 | |
| select_methods | 0.105 | 0.000 | 0.106 | |
| simple_FNR_params | 0.054 | 0.000 | 0.055 | |