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lmc297 / bactaxR

Bacterial taxonomy construction and evaluation in R
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Install #1

Closed ntromas closed 4 years ago

ntromas commented 4 years ago

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’ ...

lmc297 commented 4 years ago

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 commented 4 years ago

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):

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’

Le ven. 10 avr. 2020 à 16:13, Laura Carroll notifications@github.com 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 https://github.com/lmc297/bactaxR/issues/1#issuecomment-612197774, 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: (514) 343 6111 3188 E-mail: tromas.nicolas@gmail.com tromas.nicolas@gmail.com Researchgate: NTromasPage https://www.researchgate.net/profile/Nicolas_Tromas Web: http://www.shapirolab.ca/

dv332247 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

Hi Laura and David,

Thanks!!! Will try this Monday,

Cheers,

Nico

Le sam. 18 avr. 2020 14 h 26, dv332247 notifications@github.com 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 notifications@github.com 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< https://github.com/lmc297/bactaxR/issues/1#issuecomment-615563794>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/APHNBEJTMMPANNOXCDH2VLLRNEYYBANCNFSM4MFTPQUA

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