Can't install MelonnPan -- AssocTests no longer available

Infrastructure and utilities
1

I am new to bioBakery and MelonnPan, and I am trying to download the MelonnPan package and run it on the demo dataset. However, I keep running into the error " ERROR: dependency ‘AssocTests’ is not available for package ‘melonnpan’ "

I tried to install AssocTests, but it is no longer available on CRAN as of 2025-06-13, and I have run into a continuous loop of downloading outdated dependencies and packages trying to get AssocTests to install and eventually be able to use MelonnPan. I tried to download an older version of R or older versions of AssocTests, but I’ve had no luck. Is there a way around this issue?

Thank you!

2

Hi @juliacapperella,

The best solution at this time is to install that package from source using their archive. You should be able to achieve this with the following code:

url <- "https://cran.r-project.org/src/contrib/Archive/AssocTests/AssocTests_1.0-1.tar.gz"
pkgFile <- "AssocTests_1.0-1.tar.gz"
download.file(url = url, destfile = pkgFile)

install.packages(pkgs=pkgFile, type="source", repos=NULL)
unlink(pkgFile)

Hope that works.

Cheers,
Jacob

3

Hi Jacob,

Thank you for your reply! Unfortunately, I tried to use the archive package and fell down a rabbit hole of other packages not being installed to download the archive, for example:

ERROR: dependency ‘fExtremes’ is not available for package ‘AssocTests’

And when I try to download fExtremes I get another error that a different (also archived) dependency is required, and so on.

Is there anything else I can do?

4

Hi @juliacapperella ,
Thank you for the heads up on the MenlonnPan issue. We are currently working on the fixing the dependency issue and will update you here asap.

Regards,
Sagun

5

Hi all, I just wanted to say that I had the same issue with AssocTests, but then I ran the code that @nearinj provided and subsequent installs and runs of melonpann were successful. It may be worth another try.

1 Like
6

Hello!

I’ve attempted to use MelonnPan but have run into the same issue. I also ran the code that was provided but run into a similar error.

url ← “``https://cran.r-project.org/src/contrib/Archive/AssocTests/AssocTests_1.0-1.tar.gz”
pkgFile ← “AssocTests_1.0-1.tar.gz”
download.file(url = url, destfile = pkgFile)

trying URL ‘``https://cran.r-project.org/src/contrib/Archive/AssocTests/AssocTests_1.0-1.tar.gz’
Content type ‘application/x-gzip’ length 802281 bytes (783 KB)
==================================================
downloaded 783 KB

install.packages(pkgs=pkgFile, type=“source”, repos=NULL)

ERROR: dependencies ‘combinat’, ‘fExtremes’ are not available for package ‘AssocTests’
Perhaps try a variation of:
install.packages(c(‘combinat’, ‘fExtremes’))

removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/AssocTests’
Warning message:
In utils::install.packages(pkgs = pkgFile, type = “source”, repos = NULL) :
installation of package ‘AssocTests_1.0-1.tar.gz’ had non-zero exit status

Is there anyway around this? Thank you!