Trouble installing dartRbase due to snpStats

[Yi Fang Tan]

Hi,

I have R version 4.5.2 installed, and have been trying to install dartRverse. When I loaded dartR.base, I ran into the error  ‘snpStats’ is not available for this version of R .

Since it's relatively short, I pasted the entire code from the installation till the load packages, in case it's helpful. I followed instructions listed in this link (http://georges.biomatix.org/storage/app/media/uploaded-files/Tutorial_2_dartR_Installation_25-Feb-24.pdf). Please let me know how I can get snpStats installed, should I try an older version of R?

Thank you in advance for your time!

Sincerely,

Clare 

  install.packages("devtools") Installing package into ‘C:/Users/hphel/AppData/Local/R/win-library/4.5’ (as ‘lib’ is unspecified)trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/devtools_2.4.6.zip' Content type 'application/zip' length 466221 bytes (455 KB) downloaded 455 KB package ‘devtools’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\hphel\AppData\Local\Temp\RtmpK6ShUO\downloaded_packages > install.packages("BiocManager") Installing package into ‘C:/Users/hphel/AppData/Local/R/win-library/4.5’ (as ‘lib’ is unspecified)trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/BiocManager_1.30.27.zip' Content type 'application/zip' length 663921 bytes (648 KB) downloaded 648 KB package ‘BiocManager’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\hphel\AppData\Local\Temp\RtmpK6ShUO\downloaded_packages > BiocManager::install("SNPRelate") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.22 (BiocManager 1.30.27), R 4.5.2 (2025-10-31 ucrt) Installing package(s) 'SNPRelate'trying URL 'https://bioconductor.org/packages/3.22/bioc/bin/windows/contrib/4.5/SNPRelate_1.44.0.zip' Content type 'application/zip' length 3991418 bytes (3.8 MB) downloaded 3.8 MB package ‘SNPRelate’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\hphel\AppData\Local\Temp\RtmpK6ShUO\downloaded_packages > install.packages("dartRverse") Installing package into ‘C:/Users/hphel/AppData/Local/R/win-library/4.5’ (as ‘lib’ is unspecified)trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/dartRverse_1.0.6.zip' Content type 'application/zip' length 1685561 bytes (1.6 MB) downloaded 1.6 MB package ‘dartRverse’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\hphel\AppData\Local\Temp\RtmpK6ShUO\downloaded_packages > library(dartRverse) ********************************************** **** Welcome to dartRverse [Version 1.0.6] **** **********************************************── Not [yet] installed dartRverse packages ──────────────────────────────────────────────────────────────────────── dartRverse ── ✖ dartR.base ✖ dartR.sexlinked ✖ dartR.captive ✖ dartR.sim ✖ dartR.data ✖ dartR.spatial ✖ dartR.popgen Please note: The core dartRverse packages are not installed yet. You can install the missing core packages using: install.packages('BiocManager') BiocManager::install('SNPRelate') dartRverse_install('dartR.base',rep='CRAN') To install all packages of the dartRverse, use: dartRverse_install('all') > dartRverse_install('dartR.base',rep='CRAN') Installing dartR.base from CRAN (latest version) Installing package into ‘C:/Users/hphel/AppData/Local/R/win-library/4.5’ (as ‘lib’ is unspecified) Warning: dependency ‘snpStats’ is not available also installing the dependency ‘dartR.data’trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/dartR.data_1.0.8.zip' trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.5/dartR.base_1.0.7.zip'package ‘dartR.data’ successfully unpacked and MD5 sums checked package ‘dartR.base’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\hphel\AppData\Local\Temp\RtmpK6ShUO\downloaded_packages > library(dartR.base) Loading required package: adegenet Loading required package: ade4 /// adegenet 2.1.11 is loaded //////////// > overview: '?adegenet' > tutorials/doc/questions: 'adegenetWeb()' > bug reports/feature requests: adegenetIssues() Loading required package: ggplot2 Loading required package: dplyr Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: dartR.data **** Welcome to dartR.data [Version 1.0.8 ] **** Registered S3 method overwritten by 'SNPassoc': method from summary.haplo.glm haplo.stats Registered S3 method overwritten by 'pegas': method from print.amova ade4

Error: package or namespace load failed for ‘dartR.base’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘snpStats’

[Jose Luis Mijangos]

Hi Clare,

Could you please give the option below a try?
If it doesn’t work, I’m very happy to help further.

Cheers,

Luis 

# 1. Clean your workspace
# Menu > Session > Clear workspace

# 2. Restart your R session
# Menu > Session > Restart R

# 3. Install the necessary Bioconductor packages
install.packages("devtools")

install.packages("BiocManager")
BiocManager::install("SNPRelate")

BiocManager::install("LEA")
BiocManager::install("snpStats")
BiocManager::install("gdsfmt")
BiocManager::install("BiocGenerics")
BiocManager::install("zlibbioc")

# 4. Install dartRverse
install.packages("dartRverse")

# 5. Install the development versions of the dartRverse packages
devtools::install_github('green-striped-gecko/dartR.sexlinked@dev')
devtools::install_github('green-striped-gecko/dartR.spatial@dev')
devtools::install_github('green-striped-gecko/dartR.captive@dev')
devtools::install_github('green-striped-gecko/dartR.popgen@dev')
devtools::install_github('green-striped-gecko/dartR.base@dev')
devtools::install_github('green-striped-gecko/dartR.sim@dev')

[Yi Fang Tan]

Hi Luis,

Thank you so much for your prompt response. I followed the steps you sent but got stuck at zlibbioc. Warning pasted below. In case it's helpful, I also had to include 'force=TRUE' to install  gdsfmtand and BiocGenerics, but all other packages installed fine. 

> BiocManager::install("zlibbioc") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.22 (BiocManager 1.30.27), R 4.5.2 (2025-10-31 ucrt) Installing package(s) 'zlibbioc' Warning message: package ‘zlibbioc’ is not available for Bioconductor version '3.22' A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

Thank you!

Clare

[Jose Luis Mijangos]

Hi Clare,

It looks like the zlibbioc package has been deprecated, so it may no longer be required as a dependency for other packages. Because of that, I suggest going ahead with steps 4 and 5 below.

One small change compared with my previous message: in step 5, it’s best to install dartR.base@dev first, as the order matters slightly.

If that still doesn’t work, you can also try installing zlibbioc directly from GitHub using devtools, as shown below.

# Optional: try this only if needed 

devtools::install_github("Bioconductor/zlibbioc") 

 # 4. Install dartRverse 

install.packages("dartRverse") 

 # 5. Install the development versions of the dartRverse packages 

devtools::install_github('green-striped-gecko/dartR.base@dev') 

devtools::install_github('green-striped-gecko/dartR.spatial@dev') 

devtools::install_github('green-striped-gecko/dartR.captive@dev') 

devtools::install_github('green-striped-gecko/dartR.popgen@dev') 

devtools::install_github('green-striped-gecko/dartR.sim@dev') 

devtools::install_github('green-striped-gecko/dartR.sexlinked@dev')

If you run into any issues along the way, feel free to let me know and I’m happy to help further.

Cheers,
Luis

[Yi Fang Tan]

Hi Luis, 

I followed your new instructions and installed the dartR. packages I wanted; everything seems to be working well, thank you so much for your prompt assistance!

Sincerely,

Clare

> library(dartRverse) ********************************************** **** Welcome to dartRverse [Version 1.0.6] **** **********************************************── Core dartRverse packages ─────────────────────────────────────────────────────────────────────────────────────── dartRverse ── ✔ dartR.base 1.1.1 ✔ dartR.data 1.0.8 ── Installed dartRverse packages ──────────────────────────────────────────────────────────────────────────────── dartRverse ── ✔ dartR.captive 1.0.35 ✔ dartR.sim 0.71 ✔ dartR.popgen 1.0.6 ✔ dartR.spatial 1.0.3