Daniel Sabanés Bové
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/hermes |
| git_branch: devel |
| git_last_commit: 2f1b4a7 |
| git_last_commit_date: 2024-10-29 11:07:06 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 941/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hermes 1.11.0 (landing page) Daniel Sabanés Bové
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2025-01-04 07:04:17 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 07:14:15 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 598.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: hermes.Rcheck |
| Warnings: 7 |
##############################################################################
##############################################################################
###
### 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/hermes.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hermes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hermes’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/hermes.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... WARNING
Warning: program compiled against libxml 212 using older 211
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
Warning: program compiled against libxml 212 using older 211
* 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 20.461 0.016 20.520
diff_expression 16.206 0.191 16.435
normalize 15.108 0.064 15.475
calc_cor 7.439 0.183 7.639
lapply 4.986 0.020 5.016
* 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: 7 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/hermes.Rcheck/00check.log’
for details.
hermes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL hermes ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Warning: program compiled against libxml 212 using older 211 Creating a new generic function for ‘filter’ in package ‘hermes’ ** help Loading required namespace: hermes Warning: program compiled against libxml 212 using older 211 *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (hermes)
hermes.Rcheck/tests/test_dplyr_compatibility.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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
Loading required package: generics
Attaching package: 'generics'
The following object is masked from 'package:dplyr':
explain
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following object is masked from 'package:dplyr':
combine
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
Warning: program compiled against libxml 212 using older 211
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
13.853 0.597 14.722
hermes.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
Warning: program compiled against libxml 212 using older 211
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
153.042 1.850 155.561
hermes.Rcheck/hermes-Ex.timings
| name | user | system | elapsed | |
| GeneSpec | 0.012 | 0.004 | 0.016 | |
| HermesData-class | 0.831 | 0.071 | 0.905 | |
| annotation | 0.041 | 0.003 | 0.045 | |
| assertions | 0.003 | 0.001 | 0.003 | |
| calc_cor | 7.439 | 0.183 | 7.639 | |
| calc_pca | 4.667 | 0.160 | 4.839 | |
| cat_with_newline | 0 | 0 | 0 | |
| cbind | 0.242 | 0.015 | 0.258 | |
| check_proportion | 0.001 | 0.000 | 0.000 | |
| colMeanZscores | 2.618 | 0.024 | 2.648 | |
| colPrinComp1 | 2.012 | 0.023 | 2.041 | |
| col_data_with_genes | 0.013 | 0.000 | 0.013 | |
| connect_biomart | 0.001 | 0.000 | 0.000 | |
| control_normalize | 0.001 | 0.000 | 0.001 | |
| control_quality | 0.002 | 0.000 | 0.002 | |
| correlate | 1.099 | 0.003 | 1.105 | |
| counts | 0.06 | 0.00 | 0.06 | |
| cut_quantile | 0.004 | 0.000 | 0.004 | |
| df_cols_to_factor | 0.115 | 0.004 | 0.119 | |
| diff_expression | 16.206 | 0.191 | 16.435 | |
| draw_barplot | 1.194 | 0.052 | 1.249 | |
| draw_boxplot | 4.158 | 0.056 | 4.223 | |
| draw_genes_barplot | 1.165 | 0.000 | 1.168 | |
| draw_heatmap | 0.878 | 0.004 | 0.884 | |
| draw_libsize_densities | 1.149 | 0.008 | 1.160 | |
| draw_libsize_hist | 0.420 | 0.000 | 0.421 | |
| draw_libsize_qq | 0.865 | 0.000 | 0.867 | |
| draw_nonzero_boxplot | 0.919 | 0.000 | 0.921 | |
| draw_scatterplot | 2.530 | 0.012 | 2.548 | |
| extra_data_names | 0.001 | 0.000 | 0.002 | |
| filter | 0.140 | 0.000 | 0.139 | |
| gene_spec | 0.004 | 0.000 | 0.003 | |
| genes | 0.013 | 0.004 | 0.017 | |
| h_all_duplicated | 0 | 0 | 0 | |
| h_df_factors_with_explicit_na | 0.004 | 0.000 | 0.005 | |
| h_diff_expr_deseq2 | 20.461 | 0.016 | 20.520 | |
| h_diff_expr_voom | 1.865 | 0.008 | 1.877 | |
| h_ensembl_to_entrez_ids | 0 | 0 | 0 | |
| h_get_annotation_biomart | 0 | 0 | 0 | |
| h_get_granges_by_id | 0.001 | 0.000 | 0.000 | |
| h_get_size_biomart | 0.001 | 0.000 | 0.000 | |
| h_has_req_annotations | 0.071 | 0.004 | 0.074 | |
| h_map_pos | 0.001 | 0.000 | 0.000 | |
| h_parens | 0.001 | 0.000 | 0.000 | |
| h_pca_df_r2_matrix | 2.240 | 0.004 | 2.248 | |
| h_pca_var_rsquared | 1.945 | 0.000 | 1.950 | |
| h_short_list | 0.001 | 0.000 | 0.000 | |
| h_strip_prefix | 0.001 | 0.000 | 0.000 | |
| h_unique_labels | 0.001 | 0.000 | 0.000 | |
| inner_join_cdisc | 0.251 | 0.000 | 0.251 | |
| isEmpty | 0.019 | 0.000 | 0.020 | |
| lapply | 4.986 | 0.020 | 5.016 | |
| metadata | 0.000 | 0.000 | 0.001 | |
| normalize | 15.108 | 0.064 | 15.475 | |
| pca_cor_samplevar | 3.039 | 0.000 | 3.046 | |
| pipe | 1.770 | 0.008 | 1.940 | |
| plot_all | 1.445 | 0.015 | 1.465 | |
| prefix | 0.001 | 0.000 | 0.001 | |
| quality_flags | 0.472 | 0.008 | 0.480 | |
| query | 0 | 0 | 0 | |
| rbind | 0.066 | 0.000 | 0.065 | |
| rename | 0.041 | 0.000 | 0.040 | |
| samples | 0.001 | 0.000 | 0.001 | |
| set_tech_failure | 0.022 | 0.000 | 0.023 | |
| show | 0.006 | 0.000 | 0.006 | |
| subset | 0.064 | 0.000 | 0.064 | |
| summary | 0.063 | 0.000 | 0.063 | |
| top_genes | 0.397 | 0.000 | 0.398 | |
| wrap_in_mae | 0.182 | 0.000 | 0.183 | |