Install about bactaxr

[lmc297]

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]

Hi Laura, Thanks for your answer. Yes I had previously installed ggtree. But I still got the error. library("ggtree") Registered S3 method overwritten by 'treeio': method from root.phylo ape ggtree v1.16.6 For help: https://yulab-smu.github.io/treedata-book/ If you use ggtree in published research, please cite the most appropriate paper(s): - Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194 - Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628 Warning message: le package ‘ggtree’ a été compilé avec la version R 3.6.1

library(devtools)

Le chargement a nécessité le package : usethis

install_github("lmc297/bactaxR")

Downloading GitHub repo lmc297/bactaxR@master Skipping 1 packages not available: ggtree ✓ checking for file ‘/private/var/folders/06/m7k540fd0hq9bbhdzxshn2h40000gn/T/Rtmp7FNrZf/remotes1435868c4294f/lmc297-bactaxR-57fa45b/DESCRIPTION’ ... ─ preparing ‘bactaxR’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘bactaxR_0.1.0.tar.gz’ * 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//Rtmp7FNrZf/file1435826743745/bactaxR_0.1.0.tar.gz’ had non-zero exit status Le ven. 10 avr. 2020 à 16:13, Laura Carroll <[email protected]> a écrit :

…

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! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6DWYEYGXCLVDYGNMWDRL54W3ANCNFSM4MFTPQUA> .

-- *************************************************************** Nicolas Tromas PhD Université de Montréal Département de sciences biologiques Microbial Evolutionary Genomics Group-Laboratoire de Jesse Shapiro Pavillon Marie-Victorin 90 Vincent-d'Indy, Montréal, Québec, H2V 2S9 Phone: [phone] E-mail: [email protected] <[email protected]> Researchgate: NTromasPage <https://www.researchgate.net/profile/Nicolas_Tromas> Web: http://www.shapirolab.ca/ ***************************************************************

[dv332247]

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]

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]

Hi Laura and David, Thanks!!! Will try this Monday, Cheers, Nico Le sam. 18 avr. 2020 14 h 26, dv332247 <[email protected]> a écrit :

…

Hi Laura, No worries, I had the same issue with the program install and with all the help you've given me it's certainly the least I can do. Thanks again, David Mahoney UBC ________________________________ From: Laura Carroll ***@***.***> Sent: 17 April 2020 22:09:20 To: lmc297/bactaxR Cc: Mahoney, David; Comment Subject: Re: [lmc297/bactaxR] Install (#1) 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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub< #1 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/APHNBEJTMMPANNOXCDH2VLLRNEYYBANCNFSM4MFTPQUA >. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6GM4ROFFVFVSHQWCUTRNHWFBANCNFSM4MFTPQUA> .