version update issues

[ekarlsenayala]

I am unable to get dada2 to install in the terminal. I've tried nearly every way to install it and its not working. The latest thing I tried was

conda install bioconductor-dada2

It downloaded dada2 but not the v1.3.3

I've also tried
source("http://bioconductor.org/biocLite.R")
biocLite(suppressUpdates = FALSE)

which gives me the following error message:
1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘igraph’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘stringi’ had non-zero exit status

Let me know if there is a better way to try to download the newest version of dada2

[benjjneb]

Have you looked at the dada2 installation page? https://benjjneb.github.io/dada2/dada-installation.html

For the current version:

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("dada2", version = "3.8")

You can see more here: https://www.bioconductor.org/packages/release/bioc/html/dada2.html

An alternative is to install from GitHub:

library(devtools)
devtools::install_github("benjjneb/dada2", ref="v1.10")

[ekarlsenayala]

Yes when I tried the if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("dada2", version = "3.8") As you mentioned it gives me this message: Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘BiocParallel’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘igraph’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘stringi’ had non-zero exit status Elena Karlsen-Ayala Ph.D. Student Dept of Plant Pathology - University of Florida ekarlsenayala@ufl.edu<mailto:ekarlsenayala@ufl.edu> On Feb 14, 2019, at 4:12 PM, Benjamin Callahan <notifications@github.com<mailto:notifications@github.com>> wrote: Have you looked at the dada2 installation page? https://benjjneb.github.io/dada2/dada-installation.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__benjjneb.github.io_dada2_dada-2Dinstallation.html&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=KLojKydH7_coxmozqg-uNwI82WAqUscDeEpdlFGDvFs&m=EwjyPcpEGeANL3jSR0CH043ciOrwfb-tTb1HY7bA9-c&s=RL0r_GifjU6d18bu7ZFJy8vuY19M-PvXFmbE8Gzgsbg&e=> For the current version: To install this package, start R (version "3.5") and enter: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("dada2", version = "3.8") You can see more here: https://www.bioconductor.org/packages/release/bioc/html/dada2.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_release_bioc_html_dada2.html&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=KLojKydH7_coxmozqg-uNwI82WAqUscDeEpdlFGDvFs&m=EwjyPcpEGeANL3jSR0CH043ciOrwfb-tTb1HY7bA9-c&s=j_O7UZSbN_SbmRT09HDU8AksTsQrIxwAim8wI_-GhbU&e=> An alternative is to install from GitHub: library(devtools) devtools::install_github("benjjneb/dada2", ref="v1.10") — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_benjjneb_dada2_issues_679-23issuecomment-2D463798505&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=KLojKydH7_coxmozqg-uNwI82WAqUscDeEpdlFGDvFs&m=EwjyPcpEGeANL3jSR0CH043ciOrwfb-tTb1HY7bA9-c&s=MHISBwb5ZX4QLXsDJto5e0EH3BGReOJa6AVDlnT_lCA&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_Atb-5FlB3BwSTWjmjACS8BI7Fu05BA31f6ks5vNdEhgaJpZM4a8cOA&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=KLojKydH7_coxmozqg-uNwI82WAqUscDeEpdlFGDvFs&m=EwjyPcpEGeANL3jSR0CH043ciOrwfb-tTb1HY7bA9-c&s=rScVRP-vGGKkD5tucJx123eV_A9P6yt0uB9Xbg7Osvg&e=>.

[benjjneb]

Do you just get warnings, or does the installation fail? What happens when you try library("dada2")?

Also, can you provide info on your R installation: R.version

[wlokhorst]

I encountered the same error message for the stringi package when installing the latest version of dada2.

However, I also found that this is an issue for more people trying to install stringi (gagolews/stringi#431).
It was recently patched, so stringi can now be installed via calling the following command from within R:
devtools::install_github("gagolews/stringi")
Source: gagolews/stringi#431 (comment)