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License: BSD 3-Clause "New" or "Revised" License
An R package (ADAGEpath) to perform signature analysis using methodology from the ADAGE manuscript
License: BSD 3-Clause "New" or "Revised" License
Following the currently suggested work-around for the error that is thrown upon attempting to install the impute package due to no detectable gfortran did not lead me to resolution.
However, I could install ADAGEpath if I individually installed the impute package beforehand
install.packages("impute")
and then, when installing ADAGEpath (using either devtools or bioc) I dot not update the impute package when prompted.
I'm not sure how universal this work-around is but maybe ADAGEpath installation instructions could suggest it as a troubleshooting option?
if you have BiocInstaller already installed (and for impute, I believe this tends to be the case), it turns out that recent versions will do a smart install of github packages and dependencies where possible:
library(BiocInstaller)
biocLite("greenelab/ADAGEpath")
# BioC_mirror: https://bioconductor.org
# Using Bioconductor 3.6 (BiocInstaller 1.27.2), R 3.4.0 (2017-04-21).
# Installing github package(s) 'greenelab/ADAGEpath'
# ... time passes ...
# * installing *source* package ‘ADAGEpath’ ...
# ** R
# ** data
# *** moving datasets to lazyload DB
# ** inst
# ** preparing package for lazy loading
# ** help
# *** installing help indices
# ** building package indices
# ** installing vignettes
# ** testing if installed package can be loaded
# * DONE (ADAGEpath)
Turns out there are quite a few dependencies!
For updated versions of R (3.5 or greater), bioconductor usage has changed from
BiocInstaller::biocLite("greenelab/ADAGEpath")
to:
BiocManager::install("greenelab/ADAGEpath")
Maybe ADAGEpath installation instructions could be updated to reflect this?
When trying to build the vignettes from ADAGEpath:
devtools::install_github("greenelab/ADAGEpath", build_vignettes = TRUE, force = T)
I received the following error:
Wa Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "User input example", and the latter is "Analyze user input dataset". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘User-input-example.Rmd’
Error: Duplicate vignette titles.
Ensure that the %\VignetteIndexEntry lines in the vignette sources
correspond to the vignette titles.
Execution halted
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