Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:51:41 -0400 (Tue, 09 Apr 2019).
Package 220/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
celaref 1.1.5 Sarah Williams
| 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: celaref |
Version: 1.1.5 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:celaref.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings celaref_1.1.5.tar.gz |
StartedAt: 2019-04-08 23:15:33 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 23:19:30 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 236.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: celaref.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:celaref.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings celaref_1.1.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/celaref.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘celaref/DESCRIPTION’ ... OK * this is package ‘celaref’ version ‘1.1.5’ * 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 ... NOTE Found the following hidden files and directories: .github These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘celaref’ 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 contrast_the_group_to_the_rest: no visible global function definition for ‘new’ contrast_the_group_to_the_rest: no visible global function definition for ‘as<-’ Undefined global functions or variables: as<- new Consider adding importFrom("methods", "as<-", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 Examples with CPU or elapsed time > 5s user system elapsed contrast_each_group_to_the_rest_for_norm_ma_with_limma 13.929 0.447 0.518 contrast_each_group_to_the_rest 12.748 0.476 13.875 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/celaref.Rcheck/00check.log’ for details.
celaref.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL celaref ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘celaref’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (celaref)
celaref.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" 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(celaref) 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, colMeans, colSums, 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, 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 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("celaref") Read 100 items ══ testthat results ═══════════════════════════════════════════════════════════ OK: 35 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 81.627 0.721 30.132
celaref.Rcheck/celaref-Ex.timings
name | user | system | elapsed | |
contrast_each_group_to_the_rest | 12.748 | 0.476 | 13.875 | |
contrast_each_group_to_the_rest_for_norm_ma_with_limma | 13.929 | 0.447 | 0.518 | |
convert_se_gene_ids | 0.103 | 0.008 | 0.110 | |
get_rankstat_table | 0.172 | 0.004 | 0.175 | |
get_the_up_genes_for_all_possible_groups | 0.002 | 0.000 | 0.001 | |
get_the_up_genes_for_group | 0.000 | 0.000 | 0.001 | |
load_dataset_10Xdata | 0.146 | 0.019 | 0.178 | |
load_se_from_tables | 0.204 | 0.000 | 0.205 | |
make_ranking_violin_plot | 2.788 | 0.076 | 2.863 | |
make_ref_similarity_names | 1.82 | 0.00 | 1.82 | |
subset_cells_by_group | 0.012 | 0.000 | 0.013 | |
trim_small_groups_and_low_expression_genes | 0.081 | 0.000 | 0.082 | |