Davide Risso
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/scone |
| git_branch: RELEASE_3_16 |
| git_last_commit: ce782b3 |
| git_last_commit_date: 2022-11-01 11:15:00 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:18 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the scone package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scone.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1809/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scone 1.22.0 (landing page) Davide Risso
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: scone |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:scone.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings scone_1.22.0.tar.gz |
| StartedAt: 2023-04-10 23:48:32 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-11 00:00:58 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 745.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scone.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:scone.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings scone_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/scone.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘scone/DESCRIPTION’ ... OK * this is package ‘scone’ version ‘1.22.0’ * package encoding: UTF-8 * 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 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 ... ‘PsiNorm.Rmd’ using ‘UTF-8’... OK ‘sconeTutorial.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.16-bioc/meat/scone.Rcheck/00check.log’ for details.
scone.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL scone ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("scone")
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% (00:00:03)
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% (00:00:03)
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% (00:00:41)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:36 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 64 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 64 ]
>
> proc.time()
user system elapsed
176.085 15.945 300.236
scone.Rcheck/scone-Ex.timings
| name | user | system | elapsed | |
| CLR_FN | 0.002 | 0.000 | 0.002 | |
| DESEQ_FN | 0.001 | 0.000 | 0.001 | |
| FQ_FN | 0.002 | 0.000 | 0.002 | |
| PSINORM_FN | 0.001 | 0.000 | 0.001 | |
| PsiNorm | 0.344 | 0.004 | 0.348 | |
| SCRAN_FN | 2.355 | 0.072 | 2.427 | |
| SUM_FN | 0.000 | 0.000 | 0.001 | |
| SconeExperiment-class | 0.126 | 0.004 | 0.130 | |
| TMM_FN | 0.003 | 0.000 | 0.003 | |
| UQ_FN | 0.001 | 0.000 | 0.001 | |
| biplot_color | 0.011 | 0.000 | 0.011 | |
| biplot_interactive | 0.291 | 0.016 | 0.307 | |
| control_genes | 0.011 | 0.004 | 0.016 | |
| estimate_ziber | 0.038 | 0.000 | 0.039 | |
| factor_sample_filter | 0.05 | 0.00 | 0.05 | |
| fast_estimate_ziber | 0.028 | 0.000 | 0.028 | |
| get_bio | 0.035 | 0.000 | 0.036 | |
| get_design | 0.403 | 0.052 | 0.456 | |
| get_negconruv | 0.043 | 0.004 | 0.048 | |
| get_normalized | 0.099 | 0.012 | 0.111 | |
| get_params | 0.038 | 0.004 | 0.042 | |
| get_qc | 0.090 | 0.004 | 0.093 | |
| get_scores | 0.089 | 0.000 | 0.089 | |
| impute_expectation | 0.001 | 0.000 | 0.000 | |
| impute_null | 0.001 | 0.000 | 0.000 | |
| lm_adjust | 0.003 | 0.000 | 0.003 | |
| make_design | 0.000 | 0.001 | 0.001 | |
| metric_sample_filter | 0.003 | 0.003 | 0.005 | |
| scone | 0.188 | 0.000 | 0.188 | |
| sconeReport | 0.095 | 0.008 | 0.103 | |
| scone_easybake | 0.105 | 0.004 | 0.109 | |
| score_matrix | 0.003 | 0.000 | 0.004 | |
| select_methods | 0.105 | 0.000 | 0.106 | |
| simple_FNR_params | 0.018 | 0.004 | 0.023 | |