Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:13:35 -0400 (Wed, 16 Oct 2019).
Package 832/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
iSEE 1.4.0 Charlotte Soneson
| 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 |
Package: iSEE |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iSEE_1.4.0.tar.gz |
StartedAt: 2019-10-16 02:36:27 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:42:39 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 371.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: iSEE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:iSEE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iSEE_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/iSEE.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘iSEE/DESCRIPTION’ ... OK * this is package ‘iSEE’ version ‘1.4.0’ * 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 ‘iSEE’ 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 Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed iSEE 12.347 0.730 13.379 annotateEnsembl 9.314 0.220 10.027 synchronizeAssays 8.867 0.224 9.091 modeGating 7.808 0.252 8.063 annotateEntrez 5.366 0.168 5.534 * 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-3.9-bioc/meat/iSEE.Rcheck/00check.log’ for details.
iSEE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL iSEE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘iSEE’ ... ** 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 (iSEE)
iSEE.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-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. > library(testthat) > library(iSEE) 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 Loading required package: SingleCellExperiment > > test_check("iSEE") Loading required package: scRNAseq Loading required package: scater Loading required package: ggplot2 Attaching package: 'scater' The following object is masked from 'package:S4Vectors': rename The following object is masked from 'package:stats': filter Class: ExperimentColorMap assays(5): counts tophat_counts cufflinks_fpkm cufflinks_fpkm rsem_tpm colData(1): passes_qc_checks_s rowData(0): all_discrete(0): all_continuous(0): global_discrete(1) global_continuous(1) ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 1117 | SKIPPED: 3 | WARNINGS: 12 | FAILED: 0 ] Warning message: In .local(object, ...) : using library sizes as size factors > > proc.time() user system elapsed 115.773 1.397 117.377
iSEE.Rcheck/iSEE-Ex.timings
name | user | system | elapsed | |
ExperimentColorMap-class | 0.044 | 0.004 | 0.112 | |
annotateEnsembl | 9.314 | 0.220 | 10.027 | |
annotateEntrez | 5.366 | 0.168 | 5.534 | |
availablePanelTypes | 0.000 | 0.000 | 0.001 | |
colDataPlotDefaults | 0.458 | 0.000 | 0.584 | |
colStatTableDefaults | 0.138 | 0.000 | 0.138 | |
customDataPlotDefaults | 0.09 | 0.00 | 0.09 | |
customStatTableDefaults | 0.095 | 0.000 | 0.096 | |
featAssayPlotDefaults | 0.972 | 0.024 | 0.996 | |
heatMapPlotDefaults | 0.226 | 0.000 | 0.226 | |
iSEE | 12.347 | 0.730 | 13.379 | |
isColorMapCompatible | 3.719 | 0.132 | 3.851 | |
jitterPoints | 0.067 | 0.000 | 0.067 | |
lassoPoints | 0.006 | 0.000 | 0.005 | |
modeGating | 7.808 | 0.252 | 8.063 | |
pointDefaults | 0.431 | 0.000 | 0.431 | |
redDimPlotDefaults | 0.252 | 0.004 | 0.256 | |
rowDataPlotDefaults | 0.343 | 0.000 | 0.343 | |
rowStatTableDefaults | 0.169 | 0.000 | 0.169 | |
sampAssayPlotDefaults | 0.348 | 0.000 | 0.348 | |
selectDefaults | 0.314 | 0.008 | 0.322 | |
subsetPointsByGrid | 0.115 | 0.000 | 0.116 | |
synchronizeAssays | 8.867 | 0.224 | 9.091 | |