Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 |
Package 935/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hermes 1.9.1 (landing page) Daniel Sabanés Bové
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the hermes package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hermes.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: hermes |
Version: 1.9.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:hermes.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hermes_1.9.1.tar.gz |
StartedAt: 2024-08-27 05:39:19 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 05:49:33 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 613.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hermes.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:hermes.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hermes_1.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/hermes.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hermes/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hermes’ version ‘1.9.1’ * 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 ‘hermes’ 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 code 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed h_diff_expr_deseq2 23.404 0.251 24.122 diff_expression 16.977 0.207 17.431 normalize 13.932 0.044 14.000 calc_cor 7.865 0.410 8.407 calc_pca 4.978 0.238 5.369 lapply 5.114 0.048 5.172 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_dplyr_compatibility.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
hermes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL hermes ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘hermes’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘filter’ in package ‘hermes’ ** help Loading required namespace: hermes *** installing help indices *** copying figures ** 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 (hermes)
hermes.Rcheck/tests/test_dplyr_compatibility.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > # In order to ensure that `hermes` does not make `dplyr` functions unusable, > # we have these separate tests as we need to first load `dplyr` and then `hermes`. > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > library(hermes) Loading required package: ggfortify Loading required package: ggplot2 Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following object is masked from 'package:dplyr': count 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:dplyr': combine, intersect, setdiff, union 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice 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 Attaching package: 'hermes' The following object is masked from 'package:dplyr': filter The following object is masked from 'package:stats': filter > filter(iris, Species == "setosa") Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa 3 4.7 3.2 1.3 0.2 setosa 4 4.6 3.1 1.5 0.2 setosa 5 5.0 3.6 1.4 0.2 setosa 6 5.4 3.9 1.7 0.4 setosa 7 4.6 3.4 1.4 0.3 setosa 8 5.0 3.4 1.5 0.2 setosa 9 4.4 2.9 1.4 0.2 setosa 10 4.9 3.1 1.5 0.1 setosa 11 5.4 3.7 1.5 0.2 setosa 12 4.8 3.4 1.6 0.2 setosa 13 4.8 3.0 1.4 0.1 setosa 14 4.3 3.0 1.1 0.1 setosa 15 5.8 4.0 1.2 0.2 setosa 16 5.7 4.4 1.5 0.4 setosa 17 5.4 3.9 1.3 0.4 setosa 18 5.1 3.5 1.4 0.3 setosa 19 5.7 3.8 1.7 0.3 setosa 20 5.1 3.8 1.5 0.3 setosa 21 5.4 3.4 1.7 0.2 setosa 22 5.1 3.7 1.5 0.4 setosa 23 4.6 3.6 1.0 0.2 setosa 24 5.1 3.3 1.7 0.5 setosa 25 4.8 3.4 1.9 0.2 setosa 26 5.0 3.0 1.6 0.2 setosa 27 5.0 3.4 1.6 0.4 setosa 28 5.2 3.5 1.5 0.2 setosa 29 5.2 3.4 1.4 0.2 setosa 30 4.7 3.2 1.6 0.2 setosa 31 4.8 3.1 1.6 0.2 setosa 32 5.4 3.4 1.5 0.4 setosa 33 5.2 4.1 1.5 0.1 setosa 34 5.5 4.2 1.4 0.2 setosa 35 4.9 3.1 1.5 0.2 setosa 36 5.0 3.2 1.2 0.2 setosa 37 5.5 3.5 1.3 0.2 setosa 38 4.9 3.6 1.4 0.1 setosa 39 4.4 3.0 1.3 0.2 setosa 40 5.1 3.4 1.5 0.2 setosa 41 5.0 3.5 1.3 0.3 setosa 42 4.5 2.3 1.3 0.3 setosa 43 4.4 3.2 1.3 0.2 setosa 44 5.0 3.5 1.6 0.6 setosa 45 5.1 3.8 1.9 0.4 setosa 46 4.8 3.0 1.4 0.3 setosa 47 5.1 3.8 1.6 0.2 setosa 48 4.6 3.2 1.4 0.2 setosa 49 5.3 3.7 1.5 0.2 setosa 50 5.0 3.3 1.4 0.2 setosa > rename(iris, petal_length = Petal.Length) Sepal.Length Sepal.Width petal_length Petal.Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa 3 4.7 3.2 1.3 0.2 setosa 4 4.6 3.1 1.5 0.2 setosa 5 5.0 3.6 1.4 0.2 setosa 6 5.4 3.9 1.7 0.4 setosa 7 4.6 3.4 1.4 0.3 setosa 8 5.0 3.4 1.5 0.2 setosa 9 4.4 2.9 1.4 0.2 setosa 10 4.9 3.1 1.5 0.1 setosa 11 5.4 3.7 1.5 0.2 setosa 12 4.8 3.4 1.6 0.2 setosa 13 4.8 3.0 1.4 0.1 setosa 14 4.3 3.0 1.1 0.1 setosa 15 5.8 4.0 1.2 0.2 setosa 16 5.7 4.4 1.5 0.4 setosa 17 5.4 3.9 1.3 0.4 setosa 18 5.1 3.5 1.4 0.3 setosa 19 5.7 3.8 1.7 0.3 setosa 20 5.1 3.8 1.5 0.3 setosa 21 5.4 3.4 1.7 0.2 setosa 22 5.1 3.7 1.5 0.4 setosa 23 4.6 3.6 1.0 0.2 setosa 24 5.1 3.3 1.7 0.5 setosa 25 4.8 3.4 1.9 0.2 setosa 26 5.0 3.0 1.6 0.2 setosa 27 5.0 3.4 1.6 0.4 setosa 28 5.2 3.5 1.5 0.2 setosa 29 5.2 3.4 1.4 0.2 setosa 30 4.7 3.2 1.6 0.2 setosa 31 4.8 3.1 1.6 0.2 setosa 32 5.4 3.4 1.5 0.4 setosa 33 5.2 4.1 1.5 0.1 setosa 34 5.5 4.2 1.4 0.2 setosa 35 4.9 3.1 1.5 0.2 setosa 36 5.0 3.2 1.2 0.2 setosa 37 5.5 3.5 1.3 0.2 setosa 38 4.9 3.6 1.4 0.1 setosa 39 4.4 3.0 1.3 0.2 setosa 40 5.1 3.4 1.5 0.2 setosa 41 5.0 3.5 1.3 0.3 setosa 42 4.5 2.3 1.3 0.3 setosa 43 4.4 3.2 1.3 0.2 setosa 44 5.0 3.5 1.6 0.6 setosa 45 5.1 3.8 1.9 0.4 setosa 46 4.8 3.0 1.4 0.3 setosa 47 5.1 3.8 1.6 0.2 setosa 48 4.6 3.2 1.4 0.2 setosa 49 5.3 3.7 1.5 0.2 setosa 50 5.0 3.3 1.4 0.2 setosa 51 7.0 3.2 4.7 1.4 versicolor 52 6.4 3.2 4.5 1.5 versicolor 53 6.9 3.1 4.9 1.5 versicolor 54 5.5 2.3 4.0 1.3 versicolor 55 6.5 2.8 4.6 1.5 versicolor 56 5.7 2.8 4.5 1.3 versicolor 57 6.3 3.3 4.7 1.6 versicolor 58 4.9 2.4 3.3 1.0 versicolor 59 6.6 2.9 4.6 1.3 versicolor 60 5.2 2.7 3.9 1.4 versicolor 61 5.0 2.0 3.5 1.0 versicolor 62 5.9 3.0 4.2 1.5 versicolor 63 6.0 2.2 4.0 1.0 versicolor 64 6.1 2.9 4.7 1.4 versicolor 65 5.6 2.9 3.6 1.3 versicolor 66 6.7 3.1 4.4 1.4 versicolor 67 5.6 3.0 4.5 1.5 versicolor 68 5.8 2.7 4.1 1.0 versicolor 69 6.2 2.2 4.5 1.5 versicolor 70 5.6 2.5 3.9 1.1 versicolor 71 5.9 3.2 4.8 1.8 versicolor 72 6.1 2.8 4.0 1.3 versicolor 73 6.3 2.5 4.9 1.5 versicolor 74 6.1 2.8 4.7 1.2 versicolor 75 6.4 2.9 4.3 1.3 versicolor 76 6.6 3.0 4.4 1.4 versicolor 77 6.8 2.8 4.8 1.4 versicolor 78 6.7 3.0 5.0 1.7 versicolor 79 6.0 2.9 4.5 1.5 versicolor 80 5.7 2.6 3.5 1.0 versicolor 81 5.5 2.4 3.8 1.1 versicolor 82 5.5 2.4 3.7 1.0 versicolor 83 5.8 2.7 3.9 1.2 versicolor 84 6.0 2.7 5.1 1.6 versicolor 85 5.4 3.0 4.5 1.5 versicolor 86 6.0 3.4 4.5 1.6 versicolor 87 6.7 3.1 4.7 1.5 versicolor 88 6.3 2.3 4.4 1.3 versicolor 89 5.6 3.0 4.1 1.3 versicolor 90 5.5 2.5 4.0 1.3 versicolor 91 5.5 2.6 4.4 1.2 versicolor 92 6.1 3.0 4.6 1.4 versicolor 93 5.8 2.6 4.0 1.2 versicolor 94 5.0 2.3 3.3 1.0 versicolor 95 5.6 2.7 4.2 1.3 versicolor 96 5.7 3.0 4.2 1.2 versicolor 97 5.7 2.9 4.2 1.3 versicolor 98 6.2 2.9 4.3 1.3 versicolor 99 5.1 2.5 3.0 1.1 versicolor 100 5.7 2.8 4.1 1.3 versicolor 101 6.3 3.3 6.0 2.5 virginica 102 5.8 2.7 5.1 1.9 virginica 103 7.1 3.0 5.9 2.1 virginica 104 6.3 2.9 5.6 1.8 virginica 105 6.5 3.0 5.8 2.2 virginica 106 7.6 3.0 6.6 2.1 virginica 107 4.9 2.5 4.5 1.7 virginica 108 7.3 2.9 6.3 1.8 virginica 109 6.7 2.5 5.8 1.8 virginica 110 7.2 3.6 6.1 2.5 virginica 111 6.5 3.2 5.1 2.0 virginica 112 6.4 2.7 5.3 1.9 virginica 113 6.8 3.0 5.5 2.1 virginica 114 5.7 2.5 5.0 2.0 virginica 115 5.8 2.8 5.1 2.4 virginica 116 6.4 3.2 5.3 2.3 virginica 117 6.5 3.0 5.5 1.8 virginica 118 7.7 3.8 6.7 2.2 virginica 119 7.7 2.6 6.9 2.3 virginica 120 6.0 2.2 5.0 1.5 virginica 121 6.9 3.2 5.7 2.3 virginica 122 5.6 2.8 4.9 2.0 virginica 123 7.7 2.8 6.7 2.0 virginica 124 6.3 2.7 4.9 1.8 virginica 125 6.7 3.3 5.7 2.1 virginica 126 7.2 3.2 6.0 1.8 virginica 127 6.2 2.8 4.8 1.8 virginica 128 6.1 3.0 4.9 1.8 virginica 129 6.4 2.8 5.6 2.1 virginica 130 7.2 3.0 5.8 1.6 virginica 131 7.4 2.8 6.1 1.9 virginica 132 7.9 3.8 6.4 2.0 virginica 133 6.4 2.8 5.6 2.2 virginica 134 6.3 2.8 5.1 1.5 virginica 135 6.1 2.6 5.6 1.4 virginica 136 7.7 3.0 6.1 2.3 virginica 137 6.3 3.4 5.6 2.4 virginica 138 6.4 3.1 5.5 1.8 virginica 139 6.0 3.0 4.8 1.8 virginica 140 6.9 3.1 5.4 2.1 virginica 141 6.7 3.1 5.6 2.4 virginica 142 6.9 3.1 5.1 2.3 virginica 143 5.8 2.7 5.1 1.9 virginica 144 6.8 3.2 5.9 2.3 virginica 145 6.7 3.3 5.7 2.5 virginica 146 6.7 3.0 5.2 2.3 virginica 147 6.3 2.5 5.0 1.9 virginica 148 6.5 3.0 5.2 2.0 virginica 149 6.2 3.4 5.4 2.3 virginica 150 5.9 3.0 5.1 1.8 virginica > > proc.time() user system elapsed 13.566 0.564 14.143
hermes.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > pkg_name <- "hermes" > library(pkg_name, character.only = TRUE) Loading required package: ggfortify Loading required package: ggplot2 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches 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 Attaching package: 'hermes' The following object is masked from 'package:stats': filter > testthat::test_check(pkg_name) [ FAIL 0 | WARN 0 | SKIP 22 | PASS 827 ] ══ Skipped tests (22) ══════════════════════════════════════════════════════════ • On Bioconductor (6): 'test-connections.R:21:3', 'test-connections.R:34:3', 'test-connections.R:49:3', 'test-connections.R:90:3', 'test-connections.R:130:3', 'test-connections.R:167:3' • On CRAN (16): 'test-calc_cor.R:42:3', 'test-calc_cor.R:53:3', 'test-differential.R:124:3', 'test-draw_barplot.R:11:3', 'test-draw_boxplot.R:12:3', 'test-draw_heatmap.R:10:3', 'test-draw_scatterplot.R:15:3', 'test-graphs.R:6:3', 'test-graphs.R:14:3', 'test-graphs.R:22:3', 'test-graphs.R:31:3', 'test-graphs.R:37:3', 'test-graphs.R:45:3', 'test-graphs.R:51:3', 'test-top_genes.R:80:3', 'test-top_genes.R:87:3' [ FAIL 0 | WARN 0 | SKIP 22 | PASS 827 ] > > proc.time() user system elapsed 153.378 1.650 155.342
hermes.Rcheck/hermes-Ex.timings
name | user | system | elapsed | |
GeneSpec | 0.006 | 0.011 | 0.018 | |
HermesData-class | 0.900 | 0.054 | 0.965 | |
annotation | 0.044 | 0.007 | 0.054 | |
assertions | 0.115 | 0.004 | 0.123 | |
calc_cor | 7.865 | 0.410 | 8.407 | |
calc_pca | 4.978 | 0.238 | 5.369 | |
cat_with_newline | 0 | 0 | 0 | |
cbind | 0.258 | 0.004 | 0.262 | |
check_proportion | 0 | 0 | 0 | |
colMeanZscores | 3.862 | 0.159 | 4.161 | |
colPrinComp1 | 2.115 | 0.032 | 2.150 | |
col_data_with_genes | 0.014 | 0.000 | 0.014 | |
connect_biomart | 0 | 0 | 0 | |
control_normalize | 0.000 | 0.000 | 0.001 | |
control_quality | 0.000 | 0.002 | 0.002 | |
correlate | 1.166 | 0.001 | 1.173 | |
counts | 0.064 | 0.000 | 0.064 | |
cut_quantile | 0.005 | 0.000 | 0.005 | |
df_cols_to_factor | 0.125 | 0.000 | 0.125 | |
diff_expression | 16.977 | 0.207 | 17.431 | |
draw_barplot | 1.156 | 0.004 | 1.162 | |
draw_boxplot | 4.319 | 0.076 | 4.614 | |
draw_genes_barplot | 1.193 | 0.008 | 1.204 | |
draw_heatmap | 0.962 | 0.000 | 0.968 | |
draw_libsize_densities | 1.208 | 0.012 | 1.222 | |
draw_libsize_hist | 0.422 | 0.000 | 0.423 | |
draw_libsize_qq | 0.866 | 0.000 | 0.870 | |
draw_nonzero_boxplot | 0.937 | 0.002 | 0.941 | |
draw_scatterplot | 2.765 | 0.008 | 2.778 | |
extra_data_names | 0.000 | 0.002 | 0.002 | |
filter | 0.150 | 0.001 | 0.151 | |
gene_spec | 0.004 | 0.000 | 0.003 | |
genes | 0.012 | 0.004 | 0.016 | |
h_all_duplicated | 0 | 0 | 0 | |
h_df_factors_with_explicit_na | 0.005 | 0.000 | 0.005 | |
h_diff_expr_deseq2 | 23.404 | 0.251 | 24.122 | |
h_diff_expr_voom | 1.725 | 0.028 | 1.756 | |
h_ensembl_to_entrez_ids | 0.001 | 0.000 | 0.000 | |
h_get_annotation_biomart | 0 | 0 | 0 | |
h_get_granges_by_id | 0.000 | 0.000 | 0.001 | |
h_get_size_biomart | 0.000 | 0.000 | 0.001 | |
h_has_req_annotations | 0.075 | 0.000 | 0.075 | |
h_map_pos | 0.001 | 0.000 | 0.000 | |
h_parens | 0.001 | 0.000 | 0.000 | |
h_pca_df_r2_matrix | 2.348 | 0.060 | 2.412 | |
h_pca_var_rsquared | 2.065 | 0.032 | 2.101 | |
h_short_list | 0.000 | 0.000 | 0.001 | |
h_strip_prefix | 0.000 | 0.000 | 0.001 | |
h_unique_labels | 0.001 | 0.000 | 0.001 | |
inner_join_cdisc | 0.249 | 0.004 | 0.253 | |
isEmpty | 0.019 | 0.000 | 0.019 | |
lapply | 5.114 | 0.048 | 5.172 | |
metadata | 0 | 0 | 0 | |
normalize | 13.932 | 0.044 | 14.000 | |
pca_cor_samplevar | 3.124 | 0.032 | 3.161 | |
pipe | 1.790 | 0.008 | 1.801 | |
plot_all | 1.489 | 0.004 | 1.497 | |
prefix | 0 | 0 | 0 | |
quality_flags | 0.506 | 0.000 | 0.507 | |
query | 0.000 | 0.000 | 0.001 | |
rbind | 0.068 | 0.000 | 0.069 | |
rename | 0.042 | 0.000 | 0.042 | |
samples | 0.000 | 0.000 | 0.001 | |
set_tech_failure | 0.022 | 0.000 | 0.022 | |
show | 0.005 | 0.000 | 0.005 | |
subset | 0.064 | 0.000 | 0.065 | |
summary | 0.064 | 0.000 | 0.065 | |
top_genes | 0.417 | 0.008 | 0.426 | |
wrap_in_mae | 0.183 | 0.000 | 0.184 | |