greenelab/adagepath

An R package (ADAGEpath) to perform signature analysis using methodology from the ADAGE manuscript

adagepath's Issues

impute dependency and gfortran error

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?

biocLite("greenelab/ADAGEpath")

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!

Bioconductor installation syntax chage

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?

Error: Duplicate vignette titles

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