Can't install KEGGprofile
Entering edit mode
Sophie • 0
Last seen 14 months ago

Hi, I'm trying to install KEGGprofile to do analysis in R but it says it's not available for BioConductor 3.13 yet. But the website says it is. sessionInfo results might be a little weird since I installed a bunch of other BioConductor packages today.

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:

Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0 (2021-05-18)
Installing package(s) 'KEGGprofile'
Old packages: 'e1071', 'stringi'
Update all/some/none? [a/s/n]: n
Warning message:
In .inet_warning(msg) :
  package ‘KEGGprofile’ is not available for Bioconductor version '3.13'

sessionInfo( ) R version 4.1.0 (2021-05-18) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] devtools_2.4.1 usethis_2.0.1 limma_3.48.0

loaded via a namespace (and not attached): [1] rstudioapi_0.13 magrittr_2.0.1 pkgload_1.2.1
[4] R6_2.5.0 rlang_0.4.11 fastmap_1.1.0
[7] tools_4.1.0 pkgbuild_1.2.0 sessioninfo_1.1.1
[10] cli_2.5.0 withr_2.4.2 ellipsis_0.3.2
[13] remotes_2.3.0 rprojroot_2.0.2 lifecycle_1.0.0
[16] crayon_1.4.1 processx_3.5.2 purrr_0.3.4
[19] BiocManager_1.30.15 callr_3.7.0 fs_1.5.0
[22] ps_1.6.0 curl_4.3.1 testthat_3.0.2
[25] memoise_2.0.0 glue_1.4.2 cachem_1.0.5
[28] compiler_4.1.0 desc_1.3.0 prettyunits_1.1.1


KEGG RNASeq • 932 views
Entering edit mode

Hi Sophie, I believe this issue is known. Can you try the temporary fix suggested here? - Avoid upgrading BiocManager to 1.30.13; fix proposed Kind regards, Kevin

Entering edit mode
Last seen 4 hours ago
United States

This package isn't available because it relies on a package that has been deprecated.

The data that was included in KEGG.db has been static for many years now, and we have been saying for many releases that KEGG.db would be deprecated in lieu of the KEGGREST package, and this release it finally happened.


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