Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:15:46 -0400 (Thu, 12 Apr 2018).
Package 1260/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
scone 1.2.0 Michael Cole
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: scone |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scone_1.2.0.tar.gz |
StartedAt: 2018-04-12 02:47:32 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 02:53:49 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 377.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scone.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scone_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scone/DESCRIPTION’ ... OK * this is package ‘scone’ version ‘1.2.0’ * 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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 ‘/home/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck/00check.log’ for details.
scone.Rcheck/00install.out
* installing *source* package ‘scone’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (scone)
scone.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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 Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:base': apply > > test_check("scone") SubmitJobs |+ | 0% (00:00:00) SubmitJobs |+ | 0% (00:00:00) SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:02) 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% (00:00:02) 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% (00:00:03) 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% (00:00:20) 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: 315 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 87.520 2.380 135.933
scone.Rcheck/scone-Ex.timings
name | user | system | elapsed | |
CLR_FN | 0.000 | 0.000 | 0.002 | |
DESEQ_FN | 0.004 | 0.000 | 0.002 | |
FQ_FN | 0.084 | 0.000 | 0.087 | |
SCRAN_FN | 1.432 | 0.044 | 1.477 | |
SUM_FN | 0 | 0 | 0 | |
SconeExperiment-class | 0.308 | 0.004 | 0.311 | |
TMM_FN | 0.072 | 0.004 | 0.077 | |
UQ_FN | 0.004 | 0.000 | 0.001 | |
biplot_color | 0.004 | 0.004 | 0.009 | |
biplot_interactive | 0.644 | 0.004 | 0.663 | |
control_genes | 0.012 | 0.004 | 0.017 | |
estimate_ziber | 0.040 | 0.004 | 0.042 | |
factor_sample_filter | 0.236 | 0.004 | 0.239 | |
fast_estimate_ziber | 0.048 | 0.000 | 0.049 | |
get_bio | 0.028 | 0.000 | 0.029 | |
get_design | 0.404 | 0.000 | 0.404 | |
get_negconruv | 0.036 | 0.000 | 0.036 | |
get_normalized | 0.164 | 0.000 | 0.163 | |
get_params | 0.016 | 0.000 | 0.013 | |
get_qc | 0.040 | 0.000 | 0.038 | |
get_scores | 0.032 | 0.000 | 0.032 | |
impute_expectation | 0.000 | 0.000 | 0.002 | |
impute_null | 0 | 0 | 0 | |
lm_adjust | 0.004 | 0.000 | 0.005 | |
make_design | 0.004 | 0.000 | 0.002 | |
metric_sample_filter | 0.008 | 0.000 | 0.007 | |
scone | 0.092 | 0.000 | 0.090 | |
sconeReport | 0.052 | 0.004 | 0.055 | |
scone_easybake | 0.036 | 0.000 | 0.036 | |
score_matrix | 0.004 | 0.000 | 0.005 | |
select_methods | 0.032 | 0.000 | 0.031 | |
simple_FNR_params | 0.028 | 0.000 | 0.028 | |