Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:41:03 -0400 (Thu, 12 Apr 2018).
Package 1366/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SummarizedExperiment 1.8.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() |
Package: SummarizedExperiment |
Version: 1.8.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SummarizedExperiment_1.8.1.tar.gz |
StartedAt: 2018-04-12 10:06:07 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 10:09:03 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 175.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SummarizedExperiment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SummarizedExperiment_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SummarizedExperiment.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK * this is package ‘SummarizedExperiment’ version ‘1.8.1’ * 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 ‘SummarizedExperiment’ 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 'library' or 'require' calls in package code: ‘HDF5Array’ ‘rhdf5’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed makeSummarizedExperimentFromExpressionSet 6.714 0.193 7.106 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.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-3.6-bioc/meat/SummarizedExperiment.Rcheck/00check.log’ for details.
SummarizedExperiment.Rcheck/00install.out
* installing *source* package ‘SummarizedExperiment’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (SummarizedExperiment)
SummarizedExperiment.Rcheck/tests/run_unitTests.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-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. > require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package") 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 [1] TRUE > SummarizedExperiment:::.test() 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns RUNIT TEST PROTOCOL -- Thu Apr 12 10:08:57 2018 *********************************************** Number of test functions: 34 Number of errors: 0 Number of failures: 0 1 Test Suite : SummarizedExperiment RUnit Tests - 34 test functions, 0 errors, 0 failures Number of test functions: 34 Number of errors: 0 Number of failures: 0 Warning messages: 1: In V_recycle(value, x, x_what = "value", skeleton_what = "x") : 'length(x)' is not a multiple of 'NROW(value)' 2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") : 'length(x)' is not a multiple of 'NROW(value)' 3: In .recycle(arg, length(x), arg.label, "x") : 'weight' length is not a divisor of 'x' length 4: In .recycle(arg, length(x), arg.label, "x") : 'weight' length is not a divisor of 'x' length 5: In .deprecatedColsMessage() : Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is deprecated. Please use a range based accessor like genes(), or select() with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object instead. 6: 145 probes could not be mapped. 7: 169 probes could not be mapped. > > proc.time() user system elapsed 30.156 0.451 31.240
SummarizedExperiment.Rcheck/SummarizedExperiment-Ex.timings
name | user | system | elapsed | |
Assays-class | 0.306 | 0.024 | 0.339 | |
RangedSummarizedExperiment-class | 0.863 | 0.008 | 0.902 | |
SummarizedExperiment-class | 0.745 | 0.013 | 0.779 | |
coverage-methods | 0.217 | 0.001 | 0.224 | |
findOverlaps-methods | 0.216 | 0.001 | 0.225 | |
inter-range-methods | 0.195 | 0.001 | 0.204 | |
intra-range-methods | 0.373 | 0.001 | 0.384 | |
makeSummarizedExperimentFromDataFrame | 0.281 | 0.002 | 0.284 | |
makeSummarizedExperimentFromExpressionSet | 6.714 | 0.193 | 7.106 | |
nearest-methods | 0.728 | 0.027 | 0.771 | |
readKallisto | 0.720 | 0.013 | 0.738 | |
saveHDF5SummarizedExperiment | 0.740 | 0.010 | 0.756 | |