Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-18 11:05:49 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

CHECK results for hermes on nebbiolo1


To the developers/maintainers of the hermes package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 859/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hermes 0.99.4  (landing page)
Daniel Sabanés Bové
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/hermes
git_branch: master
git_last_commit: b43d4dc
git_last_commit_date: 2021-12-07 14:15:34 -0500 (Tue, 07 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hermes
Version: 0.99.4
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:hermes.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings hermes_0.99.4.tar.gz
StartedAt: 2022-01-17 19:29:13 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 19:35:44 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 390.2 seconds
RetCode: 0
Status:   OK  
CheckDir: hermes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:hermes.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings hermes_0.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/hermes.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hermes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hermes’ version ‘0.99.4’
* 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 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 13.697  0.120  13.817
diff_expression    10.761  0.092  10.853
normalize           9.852  0.088   9.940
calc_pca            5.071  0.668   5.739
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

hermes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL hermes
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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, 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 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 
  8.853   0.437   9.276 

hermes.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
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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, 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: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


══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (5)
• On CRAN (16)

[ FAIL 0 | WARN 0 | SKIP 21 | PASS 821 ]
> 
> proc.time()
   user  system elapsed 
105.466   1.529 106.995 

Example timings

hermes.Rcheck/hermes-Ex.timings

nameusersystemelapsed
GeneSpec0.0370.0000.038
HermesData-class0.5760.0120.588
annotation0.0370.0000.037
assertions0.0030.0000.003
calc_cor4.6000.1364.736
calc_pca5.0710.6685.739
cat_with_newline0.0000.0000.001
cbind0.1580.0000.159
check_proportion000
colMeanZscores1.5870.0351.622
colPrinComp11.2020.0121.214
col_data_with_genes0.010.000.01
connect_biomart000
control_normalize0.0010.0000.000
control_quality0.0040.0000.003
correlate0.6560.0160.672
counts0.0390.0040.043
cut_quantile0.0040.0000.004
df_cols_to_factor0.0770.0000.077
diff_expression10.761 0.09210.853
draw_barplot0.7600.0080.768
draw_boxplot2.5030.0482.551
draw_genes_barplot0.7930.0160.809
draw_libsize_densities0.8230.0000.823
draw_libsize_hist0.3040.0160.320
draw_libsize_qq0.5850.0000.585
draw_nonzero_boxplot0.5740.0000.574
draw_scatterplot1.6360.0161.653
extra_data_names0.0000.0020.002
filter0.1200.0130.133
gene_spec0.0030.0000.003
genes0.0150.0480.063
h_all_duplicated0.0000.0000.001
h_df_factors_with_explicit_na0.0030.0000.003
h_diff_expr_deseq213.697 0.12013.817
h_diff_expr_voom1.0380.0041.042
h_ensembl_to_entrez_ids000
h_get_annotation_biomart000
h_get_granges_by_id000
h_get_size_biomart000
h_has_req_annotations0.0490.0020.051
h_map_pos000
h_parens000
h_pca_df_r2_matrix1.3790.0161.395
h_pca_var_rsquared1.2100.0121.222
h_short_list0.0000.0000.001
h_strip_prefix0.0000.0000.001
h_unique_labels0.0010.0000.001
inner_join_cdisc0.1440.0080.152
isEmpty0.0150.0000.015
lapply3.3120.0443.356
metadata0.0010.0000.000
normalize9.8520.0889.940
pca_cor_samplevar1.8170.0121.829
pipe1.1160.0121.128
plot_all0.9710.0120.983
prefix0.0000.0000.001
quality_flags0.1540.0000.154
query0.0000.0000.001
rbind0.0430.0000.044
rename0.0210.0000.021
samples0.0010.0000.001
set_tech_failure0.0170.0000.016
show0.0000.0040.004
subset0.0470.0000.047
summary0.0430.0000.043
top_genes0.2680.0000.269
wrap_in_mae0.2620.0200.330