# From CRAN
# install.packages("package-name")
library(dplyr)
library(purrr)
library(tidyxl)
# Dev versions of packages from rOpenSci
# remotes::install_github("ropensci/packagename")
library(rfishbase)
library(rgbif)
library(helminthR)
# Bioconductor
# Install instructions here: https://bioconductor.org/install/
# BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))
library(GenomicFeatures)
library(AnnotationDbi)
tl;dr
You can get information about your R session using several different functions.
Session info?
What
Session info is just some details about your working environment like your version of R, the locale it’s running from and any loaded packages.
It gives a snapshot to help people reproduce what you’ve done or spot any anomalies. You might get asked for this if someone is diagnosing your R problem. You may also see it at the end of blog posts or reports.
You might typically print this to the console with the base function sessionInfo(), but it gives a lot of information by default. Other functions have been created to make the output more friendly.
This post
I’ve been using sessionInfo(), but read about Yihui’s session_info() function in his {xfun} package and saw Mat at machinegurning.com using session_info() from {devtools}.
I want to see the outputs side-by-side for my own curiosity.
Load packages
Let’s grab some packages from different sources to see how they’re represented in the output of each session info function.
Click to expand package-installation details
For a bit of diversity, I’ve grabbed some packages from:
- CRAN – the typical source for R packages
- GitHub – for packages in development or that haven’t had a release anywhere else
- Bioconductor – an open-dev project for packages ‘for the analysis and comprehension of high-throughput genomic data’
Functions demo
We’ll be looking at:
Click the package name to jump to that section.
Note
I later re-rendered this post, so the output from each function will show a date after the initial publication date of this post
1. Using {utils}
From the documentation for the function:
Print version information about R, the OS and attached or loaded packages.
What do you get? Loads of stuff:
- R version, platform and OS
- matrix products, BLAS and LAPACK
- locale (where you’re running R from)
- packages – attached base packages, other attached packages, and loaded packages via namespace (but not attached) in separate sections with their version numbers
Maybe that’s too much stuff. Also I don’t really know what the BLAS and LAPACK stuff is; something to do with linear algebra. There’s also no notation to say where the packages came from (CRAN, GitHub or Bioconductor). But it’s pretty human-readable.
Click to expand the output from this function
utils::sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicFeatures_1.52.1 AnnotationDbi_1.62.2 Biobase_2.60.0
[4] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1 IRanges_2.34.1
[7] S4Vectors_0.38.1 BiocGenerics_0.46.0 helminthR_1.0.10
[10] rgbif_3.7.7.2 rfishbase_4.1.2 tidyxl_1.0.8
[13] purrr_1.0.1 dplyr_1.1.2
loaded via a namespace (and not attached):
[1] DBI_1.1.3 bitops_1.0-7
[3] biomaRt_2.56.1 rlang_1.1.1
[5] magrittr_2.0.3 matrixStats_1.0.0
[7] compiler_4.3.1 RSQLite_2.3.1
[9] png_0.1-8 vctrs_0.6.3
[11] rvest_1.0.3 stringr_1.5.0
[13] pkgconfig_2.0.3 crayon_1.5.2
[15] fastmap_1.1.1 dbplyr_2.3.3
[17] XVector_0.40.0 fontawesome_0.5.1
[19] utf8_1.2.3 Rsamtools_2.16.0
[21] rmarkdown_2.23 tzdb_0.4.0
[23] bit_4.0.5 xfun_0.39
[25] zlibbioc_1.46.0 cachem_1.0.8
[27] jsonlite_1.8.7 progress_1.2.2
[29] blob_1.2.4 DelayedArray_0.26.7
[31] BiocParallel_1.34.2 parallel_4.3.1
[33] prettyunits_1.1.1 R6_2.5.1
[35] stringi_1.7.12 rtracklayer_1.60.0
[37] Rcpp_1.0.11 SummarizedExperiment_1.30.2
[39] knitr_1.43.1 readr_2.1.4
[41] Matrix_1.6-0 tidyselect_1.2.0
[43] rstudioapi_0.15.0 abind_1.4-5
[45] yaml_2.3.7 codetools_0.2-19
[47] curl_5.0.1 lattice_0.21-8
[49] tibble_3.2.1 plyr_1.8.8
[51] KEGGREST_1.40.0 evaluate_0.21
[53] BiocFileCache_2.8.0 xml2_1.3.5
[55] Biostrings_2.68.1 pillar_1.9.0
[57] filelock_1.0.2 MatrixGenerics_1.12.3
[59] whisker_0.4.1 generics_0.1.3
[61] RCurl_1.98-1.12 hms_1.1.3
[63] ggplot2_3.4.2 munsell_0.5.0
[65] scales_1.2.1 glue_1.6.2
[67] lazyeval_0.2.2 tools_4.3.1
[69] BiocIO_1.10.0 data.table_1.14.8
[71] GenomicAlignments_1.36.0 fs_1.6.3
[73] XML_3.99-0.14 grid_4.3.1
[75] colorspace_2.1-0 GenomeInfoDbData_1.2.10
[77] restfulr_0.0.15 cli_3.6.1
[79] rappdirs_0.3.3 fansi_1.0.4
[81] S4Arrays_1.0.5 gtable_0.3.3
[83] oai_0.4.0 digest_0.6.33
[85] rjson_0.2.21 htmlwidgets_1.6.2
[87] memoise_2.0.1 htmltools_0.5.5
[89] lifecycle_1.0.3 httr_1.4.6
[91] bit64_4.0.5 2. Using {devtools}
From the documentation for the function:
This is
sessionInfo()re-written from scratch to both exclude data that’s rarely useful (e.g., the full collate string or base packages loaded) and include stuff you’d like to know (e.g., where a package was installed from).
What do you get? You get basically what’s in sessionInfo()
- sections split into ‘session info’ and ‘packages’
- version, system, UI, language, locale, timezone and date
- package names with version number, date and source (CRAN, Bioconductor, GitHub, local)
It’s even more human-readable in the packages section, where the output is in table format and in alphabetical order. In particular, there’s a column to tell you where the package came from. For example, see how the {helminthR} package is from github (ropensci/helminthR@549957a) (i.e. the development version with a specific Git ref hash) and there’s an asterisk in the row to show you it was attached in the session.
Click to expand the output from this function
devtools::session_info()─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.3.1 (2023-06-16)
os macOS Ventura 13.2.1
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/London
date 2023-08-08
pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
AnnotationDbi * 1.62.2 2023-07-02 [1] Bioconductor
Biobase * 2.60.0 2023-05-08 [1] Bioconductor
BiocFileCache 2.8.0 2023-05-08 [1] Bioconductor
BiocGenerics * 0.46.0 2023-06-04 [1] Bioconductor
BiocIO 1.10.0 2023-05-08 [1] Bioconductor
BiocParallel 1.34.2 2023-05-28 [1] Bioconductor
biomaRt 2.56.1 2023-06-11 [1] Bioconductor
Biostrings 2.68.1 2023-05-21 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.1)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
curl 5.0.1 2023-06-07 [1] CRAN (R 4.3.0)
data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
dbplyr 2.3.3 2023-07-07 [1] CRAN (R 4.3.0)
DelayedArray 0.26.7 2023-07-30 [1] Bioconductor
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.0)
dplyr * 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
fontawesome 0.5.1 2023-04-18 [1] CRAN (R 4.3.0)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.36.1 2023-07-02 [1] Bioconductor
GenomeInfoDbData 1.2.10 2023-08-08 [1] Bioconductor
GenomicAlignments 1.36.0 2023-05-08 [1] Bioconductor
GenomicFeatures * 1.52.1 2023-07-02 [1] Bioconductor
GenomicRanges * 1.52.0 2023-05-08 [1] Bioconductor
ggplot2 3.4.2 2023-04-03 [1] CRAN (R 4.3.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
helminthR * 1.0.10 2023-08-08 [1] Github (ropensci/helminthR@549957a)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
httr 1.4.6 2023-05-08 [1] CRAN (R 4.3.0)
IRanges * 2.34.1 2023-07-02 [1] Bioconductor
jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.0)
KEGGREST 1.40.0 2023-05-08 [1] Bioconductor
knitr 1.43.1 2023-06-21 [1] https://yihui.r-universe.dev (R 4.3.1)
later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
Matrix 1.6-0 2023-07-08 [1] CRAN (R 4.3.0)
MatrixGenerics 1.12.3 2023-07-30 [1] Bioconductor
matrixStats 1.0.0 2023-06-02 [1] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
oai 0.4.0 2022-11-10 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.2 2023-06-26 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgload 1.3.2.1 2023-07-08 [1] CRAN (R 4.3.0)
plyr 1.8.8 2022-11-11 [1] CRAN (R 4.3.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.0)
processx 3.8.2 2023-06-30 [1] CRAN (R 4.3.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.3.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.0)
RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
readr 2.1.4 2023-02-10 [1] CRAN (R 4.3.0)
remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
rfishbase * 4.1.2 2023-06-02 [1] CRAN (R 4.3.0)
rgbif * 3.7.7.2 2023-08-08 [1] Github (ropensci/rgbif@3bdfdb2)
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
rmarkdown 2.23 2023-07-01 [1] CRAN (R 4.3.0)
Rsamtools 2.16.0 2023-06-04 [1] Bioconductor
RSQLite 2.3.1 2023-04-03 [1] CRAN (R 4.3.0)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
rtracklayer 1.60.0 2023-05-08 [1] Bioconductor
rvest 1.0.3 2022-08-19 [1] CRAN (R 4.3.0)
S4Arrays 1.0.5 2023-07-30 [1] Bioconductor
S4Vectors * 0.38.1 2023-05-08 [1] Bioconductor
scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
shiny 1.7.4.1 2023-07-06 [1] CRAN (R 4.3.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
SummarizedExperiment 1.30.2 2023-06-11 [1] Bioconductor
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
tidyxl * 1.0.8 2022-09-01 [1] CRAN (R 4.3.0)
tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
usethis 2.2.2 2023-07-06 [1] CRAN (R 4.3.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0)
vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.3.0)
whisker 0.4.1 2022-12-05 [1] CRAN (R 4.3.0)
xfun 0.39 2023-04-20 [1] CRAN (R 4.3.0)
XML 3.99-0.14 2023-03-19 [1] CRAN (R 4.3.0)
xml2 1.3.5 2023-07-06 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector 0.40.0 2023-05-08 [1] Bioconductor
yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
zlibbioc 1.46.0 2023-05-08 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
──────────────────────────────────────────────────────────────────────────────3. Using {sessioninfo}
From the CRAN page for the package:
It is similar to
utils::sessionInfo(), but includes more information about packages, and where they were installed from.
What do you get? Basically the same as utils::sessionInfo(). Note that the final column of output – the source column is wrapped below.
Click to expand the output from this function
sessioninfo::session_info()─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.3.1 (2023-06-16)
os macOS Ventura 13.2.1
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/London
date 2023-08-08
pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
AnnotationDbi * 1.62.2 2023-07-02 [1] Bioconductor
Biobase * 2.60.0 2023-05-08 [1] Bioconductor
BiocFileCache 2.8.0 2023-05-08 [1] Bioconductor
BiocGenerics * 0.46.0 2023-06-04 [1] Bioconductor
BiocIO 1.10.0 2023-05-08 [1] Bioconductor
BiocParallel 1.34.2 2023-05-28 [1] Bioconductor
biomaRt 2.56.1 2023-06-11 [1] Bioconductor
Biostrings 2.68.1 2023-05-21 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.1)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
curl 5.0.1 2023-06-07 [1] CRAN (R 4.3.0)
data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
dbplyr 2.3.3 2023-07-07 [1] CRAN (R 4.3.0)
DelayedArray 0.26.7 2023-07-30 [1] Bioconductor
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.0)
dplyr * 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
fontawesome 0.5.1 2023-04-18 [1] CRAN (R 4.3.0)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.36.1 2023-07-02 [1] Bioconductor
GenomeInfoDbData 1.2.10 2023-08-08 [1] Bioconductor
GenomicAlignments 1.36.0 2023-05-08 [1] Bioconductor
GenomicFeatures * 1.52.1 2023-07-02 [1] Bioconductor
GenomicRanges * 1.52.0 2023-05-08 [1] Bioconductor
ggplot2 3.4.2 2023-04-03 [1] CRAN (R 4.3.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
helminthR * 1.0.10 2023-08-08 [1] Github (ropensci/helminthR@549957a)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
httr 1.4.6 2023-05-08 [1] CRAN (R 4.3.0)
IRanges * 2.34.1 2023-07-02 [1] Bioconductor
jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.0)
KEGGREST 1.40.0 2023-05-08 [1] Bioconductor
knitr 1.43.1 2023-06-21 [1] https://yihui.r-universe.dev (R 4.3.1)
later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
Matrix 1.6-0 2023-07-08 [1] CRAN (R 4.3.0)
MatrixGenerics 1.12.3 2023-07-30 [1] Bioconductor
matrixStats 1.0.0 2023-06-02 [1] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
oai 0.4.0 2022-11-10 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.2 2023-06-26 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgload 1.3.2.1 2023-07-08 [1] CRAN (R 4.3.0)
plyr 1.8.8 2022-11-11 [1] CRAN (R 4.3.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.0)
processx 3.8.2 2023-06-30 [1] CRAN (R 4.3.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.3.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.0)
RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
readr 2.1.4 2023-02-10 [1] CRAN (R 4.3.0)
remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
rfishbase * 4.1.2 2023-06-02 [1] CRAN (R 4.3.0)
rgbif * 3.7.7.2 2023-08-08 [1] Github (ropensci/rgbif@3bdfdb2)
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
rmarkdown 2.23 2023-07-01 [1] CRAN (R 4.3.0)
Rsamtools 2.16.0 2023-06-04 [1] Bioconductor
RSQLite 2.3.1 2023-04-03 [1] CRAN (R 4.3.0)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
rtracklayer 1.60.0 2023-05-08 [1] Bioconductor
rvest 1.0.3 2022-08-19 [1] CRAN (R 4.3.0)
S4Arrays 1.0.5 2023-07-30 [1] Bioconductor
S4Vectors * 0.38.1 2023-05-08 [1] Bioconductor
scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
shiny 1.7.4.1 2023-07-06 [1] CRAN (R 4.3.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
SummarizedExperiment 1.30.2 2023-06-11 [1] Bioconductor
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
tidyxl * 1.0.8 2022-09-01 [1] CRAN (R 4.3.0)
tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
usethis 2.2.2 2023-07-06 [1] CRAN (R 4.3.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0)
vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.3.0)
whisker 0.4.1 2022-12-05 [1] CRAN (R 4.3.0)
xfun 0.39 2023-04-20 [1] CRAN (R 4.3.0)
XML 3.99-0.14 2023-03-19 [1] CRAN (R 4.3.0)
xml2 1.3.5 2023-07-06 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector 0.40.0 2023-05-08 [1] Bioconductor
yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
zlibbioc 1.46.0 2023-05-08 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
──────────────────────────────────────────────────────────────────────────────4. Using {xfun}
From Yihui Xie’s Introduction to {xfun} page:
…it is rarely useful to print out the names of base R packages, or information about the matrix products / BLAS / LAPACK. Often times I want additional information in the session information, such as the Pandoc version when rmarkdown is used.
What do you get? Basically utils::sessionInfo() but no matrix products, BLAS or LAPACK info, plus all the packages are listed together with their version numbers. You also can’t see where the package came from (CRAN, GitHub or Bioconductor). It lacks some human-readability compared to the functions in {devtools} and {sessioninfo}, but is clearly enough for Yihui – his package contains ‘miscellaneous functions that [he] use[s] by [him]self from time to time’.
Click to expand the output from this function
xfun::session_info()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1
Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8
time zone: Europe/London
tzcode source: internal
Package version:
abind_1.4-5 AnnotationDbi_1.62.2
ape_5.7.1 askpass_1.1
assertthat_0.2.1 backports_1.4.1
base64enc_0.1.3 BH_1.81.0.1
Biobase_2.60.0 BiocFileCache_2.8.0
BiocGenerics_0.46.0 BiocIO_1.10.0
BiocParallel_1.34.2 biomaRt_2.56.1
Biostrings_2.68.1 bit_4.0.5
bit64_4.0.5 bitops_1.0-7
blob_1.2.4 bold_1.3.0
brew_1.0.8 brio_1.1.3
bslib_0.5.0 cachem_1.0.8
callr_3.7.3 checkmate_2.2.0
cli_3.6.1 clipr_0.8.0
cluster_2.1.4 codetools_0.2-19
colorspace_2.1-0 commonmark_1.9.0
compiler_4.3.1 conditionz_0.1.0
contentid_0.0.17 cpp11_0.4.5
crayon_1.5.2 credentials_1.3.2
crul_1.4.0 curl_5.0.1
data.table_1.14.8 DBI_1.1.3
dbplyr_2.3.3 DelayedArray_0.26.7
desc_1.4.2 devtools_2.4.5
diffobj_0.3.5 digest_0.6.33
downlit_0.4.3 dplyr_1.1.2
duckdb_0.8.1.1 ellipsis_0.3.2
evaluate_0.21 fansi_1.0.4
farver_2.1.1 fastmap_1.1.1
fastmatch_1.1.3 filelock_1.0.2
fontawesome_0.5.1 foreach_1.5.2
foreign_0.8.84 formatR_1.14
Formula_1.2.5 fs_1.6.3
futile.logger_1.4.3 futile.options_1.0.1
generics_0.1.3 GenomeInfoDb_1.36.1
GenomeInfoDbData_1.2.10 GenomicAlignments_1.36.0
GenomicFeatures_1.52.1 GenomicRanges_1.52.0
gert_1.9.3 ggplot2_3.4.2
gh_1.4.0 gitcreds_0.1.2
glue_1.6.2 graphics_4.3.1
grDevices_4.3.1 grid_4.3.1
gridExtra_2.3 gtable_0.3.3
helminthR_1.0.10 highr_0.10
Hmisc_5.1.0 hms_1.1.3
htmlTable_2.4.1 htmltools_0.5.5
htmlwidgets_1.6.2 httpcode_0.3.0
httpuv_1.6.11 httr_1.4.6
httr2_0.2.3 igraph_1.5.0.1
ini_0.3.1 IRanges_2.34.1
isoband_0.2.7 iterators_1.0.14
jquerylib_0.1.4 jsonlite_1.8.7
KEGGREST_1.40.0 knitr_1.43.1
labeling_0.4.2 lambda.r_1.2.4
later_1.3.1 lattice_0.21-8
lazyeval_0.2.2 lifecycle_1.0.3
magrittr_2.0.3 MASS_7.3.60
Matrix_1.6-0 MatrixGenerics_1.12.3
matrixStats_1.0.0 memoise_2.0.1
methods_4.3.1 mgcv_1.9.0
mime_0.12 miniUI_0.1.1.1
munsell_0.5.0 natserv_1.0.0
nlme_3.1.162 nnet_7.3.19
oai_0.4.0 openssl_2.1.0
parallel_4.3.1 pbapply_1.7.2
phangorn_2.11.1 pillar_1.9.0
piton_1.0.0 pkgbuild_1.4.2
pkgconfig_2.0.3 pkgdown_2.0.7
pkgload_1.3.2.1 plogr_0.2.0
plyr_1.8.8 png_0.1-8
praise_1.0.0 prettyunits_1.1.1
processx_3.8.2 profvis_0.3.8
progress_1.2.2 promises_1.2.0.1
ps_1.7.5 purrr_1.0.1
quadprog_1.5.8 R6_2.5.1
ragg_1.2.5 rappdirs_0.3.3
ratelimitr_0.4.1 rcmdcheck_1.4.0
RColorBrewer_1.1.3 Rcpp_1.0.11
RCurl_1.98-1.12 readr_2.1.4
rematch2_2.1.2 remotes_2.4.2.1
rentrez_1.2.3 restfulr_0.0.15
rex_1.2.1 rfishbase_4.1.2
rgbif_3.7.7.2 Rhtslib_2.2.0
ritis_1.0.0 rjson_0.2.21
rlang_1.1.1 rmarkdown_2.23
rncl_0.8.7 rotl_3.1.0
roxygen2_7.2.3 rpart_4.1.19
rprojroot_2.0.3 rredlist_0.7.1
Rsamtools_2.16.0 RSQLite_2.3.1
rstudioapi_0.15.0 rtracklayer_1.60.0
rversions_2.1.2 rvest_1.0.3
S4Arrays_1.0.5 S4Vectors_0.38.1
sass_0.4.7 scales_1.2.1
selectr_0.4.2 sessioninfo_1.2.2
shiny_1.7.4.1 snow_0.4.4
solrium_1.2.0 sourcetools_0.1.7.1
splines_4.3.1 stats_4.3.1
stats4_4.3.1 stringi_1.7.12
stringr_1.5.0 SummarizedExperiment_1.30.2
sys_3.4.2 systemfonts_1.0.4
taxize_0.9.100 testthat_3.1.10
textshaping_0.3.6 tibble_3.2.1
tidyr_1.3.0 tidyselect_1.2.0
tidyxl_1.0.8 tinytex_0.45
tools_4.3.1 triebeard_0.4.1
tzdb_0.4.0 urlchecker_1.0.1
urltools_1.7.3 usethis_2.2.2
utf8_1.2.3 utils_4.3.1
uuid_1.1.0 vctrs_0.6.3
viridis_0.6.4 viridisLite_0.4.2
vroom_1.6.3 waldo_0.5.1
whisker_0.4.1 WikidataQueryServiceR_1.0.0
WikidataR_2.3.3 WikipediR_1.5.0
wikitaxa_0.4.0 withr_2.5.0
wk_0.7.3 worrms_0.4.3
xfun_0.39 XML_3.99-0.14
xml2_1.3.5 xopen_1.0.0
xtable_1.8-4 XVector_0.40.0
yaml_2.3.7 zip_2.3.0
zlibbioc_1.46.0 zoo_1.8.12 Conclusion
Yep, they basically do the same thing with slight differences. I personally like the idea of having some kind of table-like output for easy readability, so I’ll probably go with {devtools} as I often have it loaded anyway.
Environment
Session info
Last rendered: 2023-08-08 12:48:07 BSTR version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GenomicFeatures_1.52.1 AnnotationDbi_1.62.2 Biobase_2.60.0
[4] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1 IRanges_2.34.1
[7] S4Vectors_0.38.1 BiocGenerics_0.46.0 helminthR_1.0.10
[10] rgbif_3.7.7.2 rfishbase_4.1.2 tidyxl_1.0.8
[13] purrr_1.0.1 dplyr_1.1.2
loaded via a namespace (and not attached):
[1] DBI_1.1.3 bitops_1.0-7
[3] remotes_2.4.2.1 biomaRt_2.56.1
[5] rlang_1.1.1 magrittr_2.0.3
[7] matrixStats_1.0.0 compiler_4.3.1
[9] RSQLite_2.3.1 callr_3.7.3
[11] png_0.1-8 vctrs_0.6.3
[13] profvis_0.3.8 rvest_1.0.3
[15] stringr_1.5.0 pkgconfig_2.0.3
[17] crayon_1.5.2 fastmap_1.1.1
[19] ellipsis_0.3.2 dbplyr_2.3.3
[21] XVector_0.40.0 fontawesome_0.5.1
[23] utf8_1.2.3 promises_1.2.0.1
[25] Rsamtools_2.16.0 rmarkdown_2.23
[27] sessioninfo_1.2.2 tzdb_0.4.0
[29] ps_1.7.5 bit_4.0.5
[31] xfun_0.39 zlibbioc_1.46.0
[33] cachem_1.0.8 jsonlite_1.8.7
[35] progress_1.2.2 blob_1.2.4
[37] later_1.3.1 DelayedArray_0.26.7
[39] BiocParallel_1.34.2 parallel_4.3.1
[41] prettyunits_1.1.1 R6_2.5.1
[43] stringi_1.7.12 rtracklayer_1.60.0
[45] pkgload_1.3.2.1 Rcpp_1.0.11
[47] SummarizedExperiment_1.30.2 knitr_1.43.1
[49] usethis_2.2.2 readr_2.1.4
[51] httpuv_1.6.11 Matrix_1.6-0
[53] tidyselect_1.2.0 rstudioapi_0.15.0
[55] abind_1.4-5 yaml_2.3.7
[57] miniUI_0.1.1.1 codetools_0.2-19
[59] processx_3.8.2 curl_5.0.1
[61] pkgbuild_1.4.2 lattice_0.21-8
[63] tibble_3.2.1 plyr_1.8.8
[65] shiny_1.7.4.1 KEGGREST_1.40.0
[67] evaluate_0.21 urlchecker_1.0.1
[69] BiocFileCache_2.8.0 xml2_1.3.5
[71] Biostrings_2.68.1 pillar_1.9.0
[73] filelock_1.0.2 MatrixGenerics_1.12.3
[75] whisker_0.4.1 generics_0.1.3
[77] RCurl_1.98-1.12 hms_1.1.3
[79] ggplot2_3.4.2 munsell_0.5.0
[81] scales_1.2.1 xtable_1.8-4
[83] glue_1.6.2 lazyeval_0.2.2
[85] tools_4.3.1 BiocIO_1.10.0
[87] data.table_1.14.8 GenomicAlignments_1.36.0
[89] fs_1.6.3 XML_3.99-0.14
[91] grid_4.3.1 devtools_2.4.5
[93] colorspace_2.1-0 GenomeInfoDbData_1.2.10
[95] restfulr_0.0.15 cli_3.6.1
[97] rappdirs_0.3.3 fansi_1.0.4
[99] S4Arrays_1.0.5 gtable_0.3.3
[101] oai_0.4.0 digest_0.6.33
[103] rjson_0.2.21 htmlwidgets_1.6.2
[105] memoise_2.0.1 htmltools_0.5.5
[107] lifecycle_1.0.3 httr_1.4.6
[109] mime_0.12 bit64_4.0.5 Reuse
CC BY-NC-SA 4.0