Installation failure due to archived CRAN dependency: qs

[BigOrangeCatDylan]

Describe the bug
Fresh installation of MetaboAnalystR fails because it depends on the qs package. The core issue is that qs has been archived and removed from CRAN.

Consequently, standard installation tools (install.packages or pak) cannot resolve the dependency tree, leading to an immediate installation crash.

To Reproduce
Steps to reproduce the behavior. Run either of the following commands on a fresh environment:

# Using devtools
devtools::install_github("xia-lab/MetaboAnalystR")

# Or using pak
pak::pkg_install("xia-lab/MetaboAnalystR")

Error Message

! Could not solve package dependencies:
* xia-lab/MetaboAnalystR: Can't install dependency qs
* qs: Can't find package called qs.

[levinhein]

Dear developers,

Similar to the case above, I am also unable to install the MetaboAnalyst package due to this issue. If you have any suggestions, kindly let us know. Thanks!

[levinhein]

I noticed that qs package had a successor/newer version "qs2". I wonder if that is compatible as an alternative or if developers will use it to make it compatible for newer versions of R moving forward.

[BigOrangeCatDylan]

I tired to use devtools::install_github(), it works:)

[levinhein]

I tired to use devtools::install_github(), it works:)

Hey Dylan. Did you type the wrong command/code that you used that you say is now working?

...because as you can see, this is still exactly the same code/command that you said did not work in your first message at the top. Or is there anything different inside the parentheses? What changed, why it is now working?

Also.. may I ask what is system session info, your R version, and MetaboAnalystR version that successfully installed? Thanks!

[levinhein]

I tired to use devtools::install_github(), it works:)

...because as you have initially pointed out, it doesn't work due to qs dependency not available... Have you discovered a way to install the qs dependency?

[levinhein]

UPDATE: I used devtools::install_version("qs", version = "0.25.5", upgrade = "never") and succesfully installed qs dependency, which then led to successful installation of MetaboAnalystR.

[mkostich]

I have tried to install qs using devtools::install_version(), devtools::install_github, remotes package, as well as cloning from github followed by R CMD BUILD and R CMD INSTALL. This all failed with compilation errors unrelated to dependencies -- there looks maybe related to use of a deprecated c++ function (the function name is not found in the library specified) -- beyond the scope of this discussion. Installing qs failed on Windows 11, Ubuntu trixie with R 4.5.1 and newer compilers/headers, and Ubuntu bookworm with R 3.6.1 and the older compilers/headers. I appreciate that you are moving to qs2, which seems like the right move. Are there still dependencies on qs? It still looks to be required for building the package with the latest commit (https://github.com/xia-lab/MetaboAnalystR/commit/a14f68839fc8f3f9c18e066b3b46f65102937ca6)? I get a missing qs package error when I try to install.

[AlexHoratio]

Not an elegant solution, but I also had issues with deprecated C++ functions (check_if_native_is_ascii) when installing qs.

However, I could install a very old version of qs (0.12) successfully (using devtools::install_version("qs", version = "0.12", upgrade = "never")), and that allowed me to install MetaboAnalystR via devtools::install_github

I hope this can be fixed more effectively, though! 😝

[TrevorKMDay]

I'm not using this package, found this thread looking for loading qs for an old project I don't want to reserialize all my files for. I also went all the way back to version 0.12 as well, but was getting an endianness error (moving files between Windows and MacOS) I wasn't getting before.

The most recent version that compiled was 0.19.1, but the endianness error never resolved. So I'm just going to have to fix this other ways, but maybe testing up to ver. 0.19.1 is helpful for someone else.