cant install through R as Tax4fun no longer available

[jcmarine]

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]

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]

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]

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

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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 rstudio  2023.06.2+561 Mountain Hydrangea (desktop)
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─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                  * version     date (UTC) lib source
 abind                      1.4-5       2016-07-21 [1] CRAN (R 4.3.0)
 ade4                       1.7-22      2023-02-06 [1] CRAN (R 4.3.0)
 ALDEx2                   * 1.34.0      2023-10-26 [1] Bioconductor
 ANCOMBC                  * 2.4.0       2023-10-26 [1] Bioconductor
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 AnnotationDbi              1.64.1      2023-11-02 [1] Bioconductor
 ape                      * 5.7-1       2023-03-13 [1] CRAN (R 4.3.0)
 aplot                      0.2.2       2023-10-06 [1] CRAN (R 4.3.1)
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 BiocManager                1.30.22     2023-08-08 [1] CRAN (R 4.3.0)
 BiocNeighbors              1.20.2      2024-01-13 [1] Bioconductor 3.18 (R 4.3.2)
 BiocParallel             * 1.36.0      2023-10-26 [1] Bioconductor
 BiocSingular               1.18.0      2023-11-06 [1] Bioconductor
 biomformat               * 1.30.0      2023-10-26 [1] Bioconductor
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 bit                        4.0.5       2022-11-15 [1] CRAN (R 4.3.0)
 bit64                      4.0.5       2020-08-30 [1] CRAN (R 4.3.0)
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 blob                       1.2.4       2023-03-17 [1] CRAN (R 4.3.0)
 bluster                    1.12.0      2023-10-24 [1] Bioconductor
 boot                       1.3-30      2024-02-26 [1] CRAN (R 4.3.1)
 broom                    * 1.0.5       2023-06-09 [1] CRAN (R 4.3.0)
 cachem                     1.0.8       2023-05-01 [1] CRAN (R 4.3.0)
 Cairo                    * 1.6-2       2023-11-28 [1] CRAN (R 4.3.1)
 callr                      3.7.5       2024-02-19 [1] CRAN (R 4.3.1)
 caTools                    1.18.2      2021-03-28 [1] CRAN (R 4.3.0)
 cellranger                 1.1.0       2016-07-27 [1] CRAN (R 4.3.0)
 checkmate                  2.3.1       2023-12-04 [1] CRAN (R 4.3.1)
 circlize                   0.4.16      2024-02-20 [1] CRAN (R 4.3.1)
 class                      7.3-22      2023-05-03 [1] CRAN (R 4.3.2)
 cli                        3.6.2       2023-12-11 [1] CRAN (R 4.3.1)
 clue                       0.3-65      2023-09-23 [1] CRAN (R 4.3.1)
 cluster                    2.1.6       2023-12-01 [1] CRAN (R 4.3.1)
 codetools                  0.2-19      2023-02-01 [1] CRAN (R 4.3.2)
 coin                       1.4-3       2023-09-27 [1] CRAN (R 4.3.1)
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 ComplexHeatmap             2.18.0      2023-10-26 [1] Bioconductor
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 [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

[Aciole-David]

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]

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