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This page was generated on 2024-03-27 11:35:55 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 942/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hermes 1.6.1  (landing page)
Daniel Sabanés Bové
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/hermes
git_branch: RELEASE_3_18
git_last_commit: c301424
git_last_commit_date: 2024-03-15 04:30:37 -0400 (Fri, 15 Mar 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for hermes on nebbiolo2


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.

raw results


Summary

Package: hermes
Version: 1.6.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:hermes.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings hermes_1.6.1.tar.gz
StartedAt: 2024-03-25 23:03:57 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 23:12:10 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 492.9 seconds
RetCode: 0
Status:   OK  
CheckDir: hermes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:hermes.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings hermes_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/hermes.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘hermes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hermes’ version ‘1.6.1’
* 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 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 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 13.724  0.532  14.256
diff_expression    11.269  0.256  11.530
normalize          10.050  0.140  10.190
calc_cor            4.976  0.368   5.410
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

hermes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL hermes
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/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)

Tests output

hermes.Rcheck/tests/test_dplyr_compatibility.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.

> # 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, sort, 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 
 11.183   0.513  11.684 

hermes.Rcheck/tests/testthat.Rout


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> pkg_name <- "hermes"
> if (requireNamespace("testthat", quietly = TRUE)) {
+   library(testthat)
+   reporter <- MultiReporter$new(list(
+     CheckReporter$new(),
+     JunitReporter$new(file = "junit-result.xml")
+   ))
+   test_results <- test_check(pkg_name, reporter = reporter)
+   saveRDS(test_results, "unit_testing_results.rds")
+ }
Loading required package: hermes
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, sort, 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


[ FAIL 0 | WARN 2 | SKIP 22 | PASS 821 ]

══ 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:122:3', 'test-differential.R:130:3',
  'test-draw_barplot.R:11:3', 'test-draw_boxplot.R:12:3',
  '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 2 | SKIP 22 | PASS 821 ]
> 
> proc.time()
   user  system elapsed 
113.437   3.759 118.436 

Example timings

hermes.Rcheck/hermes-Ex.timings

nameusersystemelapsed
GeneSpec0.0100.0040.014
HermesData-class0.6730.0720.745
annotation0.0370.0040.041
assertions0.0020.0000.002
calc_cor4.9760.3685.410
calc_pca3.3510.2323.583
cat_with_newline000
cbind1.0500.1361.187
check_proportion000
colMeanZscores1.7580.1081.866
colPrinComp11.3350.0801.415
col_data_with_genes0.0130.0000.012
connect_biomart000
control_normalize0.0010.0000.001
control_quality0.0020.0000.002
correlate0.6810.0320.713
counts0.0500.0000.051
cut_quantile0.0000.0040.004
df_cols_to_factor0.1750.0040.179
diff_expression11.269 0.25611.530
draw_barplot1.0230.0201.042
draw_boxplot3.6190.0883.769
draw_genes_barplot0.9610.0881.049
draw_libsize_densities1.7170.2922.009
draw_libsize_hist0.4190.0040.423
draw_libsize_qq0.7320.0280.759
draw_nonzero_boxplot1.0550.0841.196
draw_scatterplot1.8040.0841.888
extra_data_names0.0010.0000.001
filter0.0900.0080.097
gene_spec0.0030.0000.002
genes0.0070.0120.019
h_all_duplicated0.0000.0000.001
h_df_factors_with_explicit_na0.0030.0040.007
h_diff_expr_deseq213.724 0.53214.256
h_diff_expr_voom1.0710.0721.144
h_ensembl_to_entrez_ids000
h_get_annotation_biomart000
h_get_granges_by_id0.0000.0000.001
h_get_size_biomart000
h_has_req_annotations0.0490.0000.049
h_map_pos0.0010.0000.000
h_parens000
h_pca_df_r2_matrix1.4390.0601.500
h_pca_var_rsquared1.2940.0081.302
h_short_list000
h_strip_prefix0.0010.0000.000
h_unique_labels0.0000.0000.001
inner_join_cdisc0.1650.0000.165
isEmpty0.0170.0000.016
lapply3.5580.0923.651
metadata000
normalize10.05 0.1410.19
pca_cor_samplevar2.0870.0802.168
pipe1.3120.0081.321
plot_all1.320.021.34
prefix0.0010.0000.000
quality_flags0.1220.0000.121
query000
rbind0.0540.0000.054
rename0.0250.0000.025
samples0.0000.0000.001
set_tech_failure0.0160.0000.017
show0.0010.0040.005
subset0.0490.0000.050
summary0.0440.0000.044
top_genes0.3790.0000.379
wrap_in_mae0.1820.0040.187