cant install through R as Tax4fun no longer available

jcmarine commented 9 months ago

I was trying to install MicrobimeAnalystR, and have tried through devtools and git, and tried building through R but all have the same error:

dependency 'Tax4fun' is not available for package 'MicrobiomeAnalystR'

Tax4fun appears to have been removed from github and their own website has disappeared. Is there a work around to install MicrobiomeAnalystR without Tax4fun?

Aciole-David commented 9 months ago

Hello, @jcmarine

I was able to install Tax4fun right now (2024-02-01 10:18:31 -03) using:

#install.packages("remotes")
remotes::install_github("kylebittinger/qiimer")
remotes::install_github("nick-youngblut/Tax4Fun")

#library(Tax4Fun)
#packageVersion(pkg = 'Tax4Fun')
#‘0.3.1’

From here: https://rdrr.io/github/nick-youngblut/Tax4Fun/ https://rdrr.io/github/kylebittinger/qiimer/

I remember having a lot of dependencies loop some years ago when I worked with MicrobiomeAnalystR...

ycliang22 commented 7 months ago

Hi, but how come you still can install microbiomeAnalystR? I used your code to install Tax4Fun, but not working with microbiomeAnalystR package.

could you please let me know how to do it? thanks!

scilexenko commented 7 months ago

Same problem here ! Keep me posted, please. Cheers, Ivan

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─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                  * version     date (UTC) lib source
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 SparseArray                1.2.4       2024-02-10 [1] Bioconductor 3.18 (R 4.3.2)
 sparseMatrixStats          1.14.0      2023-10-26 [1] Bioconductor
 spatial                    7.3-17      2023-07-20 [1] CRAN (R 4.3.2)
 splitstackshape          * 1.4.8       2019-04-21 [1] CRAN (R 4.3.0)
 stable                     1.1.6       2022-03-02 [1] CRAN (R 4.3.0)
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 statip                     0.2.3       2019-11-17 [1] CRAN (R 4.3.0)
 statmod                    1.5.0       2023-01-06 [1] CRAN (R 4.3.0)
 stringfish                 0.16.0      2023-11-28 [1] CRAN (R 4.3.1)
 stringi                    1.8.3       2023-12-11 [1] CRAN (R 4.3.1)
 stringr                  * 1.5.1       2023-11-14 [1] CRAN (R 4.3.1)
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 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

Aciole-David commented 7 months ago

Hello, For those asking, this is my 7 steps install scheme for Windows (tested 10 / 11 some time ago)

Can't guarantee it gonna work for everyone

Please remember that this is just a hint; @xia-lab folks can give better/official answers

Good luck

library(BiocManager)

# Step 1: devtools
#install.packages("devtools")
library(devtools)

# Step2: pacman
#install.packages("pacman")
library(pacman)

pacman::p_load(phyloseq, metacoder, pryr, biomformat, RColorBrewer, ggplot2, gplots, Cairo, igraph, igraph, BiocParallel, randomForest, metagenomeSeq, MASS, DESeq2, vegan, RJSONIO, ggfortify, pheatmap, xtable, genefilter, data.table, reshape, stringr, ape, grid, gridExtra, splitstackshape, edgeR, globaltest, R.utils, viridis, ggrepel, ppcor, qs, dplyr, limma, memoise, tidyverse)

# Step3: Rtools
#manually install compatible version of Rtools for windows
#https://cran.r-project.org/bin/windows/Rtools/

# Step4: remote repos; qiime, biom
#install.packages("remotes")
#qiimer and biom required for tax4fun
remotes::install_github("kylebittinger/qiimer", force = T)
library(qiimer)
#RJSONIO required for biom
install.packages("RJSONIO")
#https://cran.r-project.org/src/contrib/Archive/biom/biom_0.3.12.tar.gz
install.packages("biom_0.3.12.tar.gz", repos = NULL, type = "source")

# Step5: Tax4fun
#tax4fun install option 1: remotes
remotes::install_github("nick-youngblut/Tax4Fun", force = T)
library(Tax4Fun)

#tax4fun install option 2: source
#http://tax4fun.gobics.de/Tax4Fun/Tax4Fun_0.3.1.zip
install.packages("Tax4Fun_0.3.1.zip", repos = NULL, type = "win.binary")
library(Tax4Fun)

# Step6: digest
#install digest
install.packages('digest', repos='http://cran.us.r-project.org')
library(digest)

# Step 7: MicrobiomeAnalyst

#Install MicrobiomeAnalystR WITHOUT documentation
# devtools::install_github("xia-lab/MicrobiomeAnalystR", build = TRUE, build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"))

#Install MicrobiomeAnalystR WITH documentation
# devtools::install_github("xia-lab/MicrobiomeAnalystR", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"))

#Install MicrobiomeAnalystR WITH documentation
devtools::install_github("xia-lab/MicrobiomeAnalystR", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"), force = T)

library(MicrobiomeAnalystR)

joviij commented 6 months ago

For folks still running into this issue, what really helped me was this portion

Note about Tax4Fun: the older version is no longer supported on CRAN but can still be installed from nick-youngblut/Tax4Fun by ensuring the following dependencies are also installed - rhdf5; qiimer; joey711/biom.

After downloading: rhdf5; qiimer; joey711/biom and running the following command:

install.packages("remotes")  
remotes::install_github("nick-youngblut/Tax4Fun")

fixed my issue

xia-lab / MicrobiomeAnalystR

cant install through R as Tax4fun no longer available #30

Can't guarantee it gonna work for everyone

Please remember that this is just a hint; @xia-lab folks can give better/official answers