search

isoverse / isoreader

Read IRMS (Isotope Ratio Mass Spectrometry) data files into R
http://isoreader.isoverse.org
GNU General Public License v2.0
8 stars 6 forks source link

Trouble installing #151

Closed r-barnes closed 3 years ago

r-barnes commented 3 years ago

Trying install.packages('isoreader') ultimately gives:

ERROR: dependencies ‘rhdf5’, ‘feather’ are not available for package ‘isoreader’
* removing ‘/home/rick/R/x86_64-pc-linux-gnu-library/4.0/isoreader’

I haven't found rhdf5 in CRAN. Are there other steps I'm supposed to take for installation?

openjournals/joss-reviews/issues/2878

sebkopf commented 3 years ago

rhdf5 is part of bioconductor which is a separate package management system from CRAN that was originally designed for bioinformatics functionality but has become much larger since. As a bioconductor package, rhdf5 can unfortunately not be installed directly from CRAN. The line biocViews in the DESCRIPTION file should make it possible for R to figure out that it needs to look at the bioconductor package list as well but it appears this does not always get resolved correctly on all operating systems. The manual installation command for rhdf5 is

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("rhdf5")

However, your issue prompted us to simplify the dependencies and make rhdf5 and several other dependencies that are only used under specific circumstances not part of the dependency list but instead make them part of the suggested packages and check whether they are actually installed whenever needed as recommended by the CRAN guidelines (and if not yet installed, provide an informative message explaining how to install them).