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Install #1

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ntromas opened this issue Apr 10, 2020 · 5 comments
Closed

Install #1

ntromas opened this issue Apr 10, 2020 · 5 comments

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@ntromas
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ntromas commented Apr 10, 2020

Hi,

I met some issue when I tried to install your package. I tried to use source, but I met another issues.
Thanks for your help!

R version 3.6.0 (2019-04-26)
install_github("lmc297/bactaxR")
Downloading GitHub repo lmc297/bactaxR@master
Skipping 1 packages not available: ggtree
checking DESCRIPTION meta-information ...6/m7k540fd0hq9bbhdzxshn2h40000gn/T/Rtmp8b2FOu/remotes140dd92d41db/lmc297-bactaxR-57fa45b/DESCRIPTION’ ...

  • installing source package ‘bactaxR’ ...
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Erreur : (converti depuis l'avis) le package ‘ggtree’ a été compilé avec la version R 3.6.1
    Exécution arrêtée
    ERROR: lazy loading failed for package ‘bactaxR’
  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/bactaxR’
    Erreur : Failed to install 'bactaxR' from GitHub:
    (converti depuis l'avis) installation of package ‘/var/folders/06/m7k540fd0hq9bbhdzxshn2h40000gn/T//Rtmp8b2FOu/file140dd7a3e9591/bactaxR_0.1.0.tar.gz’ had non-zero exit status
@lmc297
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lmc297 commented Apr 10, 2020

Hello,

I attempted to replicate your error, and it appears that bactaxR skips the installation of ggtree, which is hosted on bioconductor. If you don't already have ggtree installed, try running the following (you may then need to re-start R/RStudio; additionally, if you do already have ggtree installed, perhaps uninstall it using remove.packages, re-install it, and possibly re-start your session):

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

BiocManager::install("ggtree")

Afterwards, try loading devtools (library(devtools)) and installing bactaxR again (install_github("lmc297/bactaxR"))

Good luck, and just let me know if this works or not!

@ntromas
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ntromas commented Apr 10, 2020 via email •
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@dv332247
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Hi ntromas,

I seem to have had the same issue as yourself. The remotes package of R (which contains install_github) has a default to convert warning messages to errors as seen with (converti depuis l'avis). If you change the default by using:
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)

That should work. All the warnings are for in this case is that the dependencies are built under different R versions which isn't a problem.

Hope that helps

@lmc297
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lmc297 commented Apr 18, 2020

Hi dv332247,
Thanks so much for finding a possible fix with Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE). I/none of the friends I've forced to test the package over the past few days have been gotten an error, so I was having difficulties replicating it. I'll update the manual with your suggestion in case others run into the same problem.
LC

@ntromas
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ntromas commented Apr 18, 2020 via email

@lmc297 lmc297 closed this as completed May 28, 2020
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@ntromas @lmc297 @dv332247