Error in installation

[christianrs5]

Hello:
I tried installing ANCOM-BC but encountered an error. I'm running R 4.2.1 and Bioconductor 3.15. I'd appreciate any ideas/suggestions on what the issue is. Thanks for developing this package!

BiocManager::install("ANCOMBC", force=TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for
details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Installing package(s) 'ANCOMBC'

There is a binary version available but the source version is later:
binary source needs_compilation
ANCOMBC 1.6.1 1.6.2 FALSE

installing the source package ‘ANCOMBC’

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/ANCOMBC_1.6.2.tar.gz'
Content type 'application/x-gzip' length 928299 bytes (906 KB)

downloaded 906 KB

• installing source package ‘ANCOMBC’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  there is no package called ‘gld’
  Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
  ERROR: lazy loading failed for package ‘ANCOMBC’
• removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ANCOMBC’

The downloaded source packages are in
‘/private/var/folders/mr/k4_62d5n7tndn56mtt1692940000gn/T/Rtmp3MHnE8/downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘ANCOMBC’ had non-zero exit status

library(ANCOMBC)
Error in library(ANCOMBC) : there is no package called ‘ANCOMBC’

[FrederickHuangLin]

Hi @christianrs5,

Could you try BiocManager::install("ANCOMBC") (without force = TRUE) and see if the issue persists?

I tried on both PC and MacBook, it seems to work.

Best,
Huang

[christianrs5]

It didn't work, but only gave me one error that the gld package couldn't be installed. I installed it separately (prior to ANCOMBC) and now it works. Looking forward to using your package now. Thanks!