krisrs1128 / multimedia

multimedia is an R package for multimodal mediation analysis of microbiome data. It has been designed to help integration of relative abundance, survey, and metabolomic data through causal mediation analysis.
https://krisrs1128.github.io/multimedia
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package installation error #1

Closed Ivy-ops closed 2 days ago

Ivy-ops commented 1 month ago

Hi developer, I met below errors upon package installation. Please advise. Thank you!

> devtools::install_github("krisrs1128/multimedia")
Downloading GitHub repo krisrs1128/multimedia@HEAD
Installing 3 packages: operator.tools, tidygraph, formula.tools
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/operator.tools_1.6.3.tgz'
Content type 'application/x-gzip' length 53416 bytes (52 KB)
==================================================
downloaded 52 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/tidygraph_1.3.1.tgz'
Content type 'application/x-gzip' length 635795 bytes (620 KB)
==================================================
downloaded 620 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/formula.tools_1.7.1.tgz'
Content type 'application/x-gzip' length 88473 bytes (86 KB)
==================================================
downloaded 86 KB

The downloaded binary packages are in
    /var/folders/zc/8vfv33l56bd_3sf0l1g729kr0000gn/T//RtmpVy8q0D/downloaded_packages
── R CMD build ──────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/zc/8vfv33l56bd_3sf0l1g729kr0000gn/T/RtmpVy8q0D/remotes488428c279c4/krisrs1128-multimedia-db174e2/DESCRIPTION’ ...
─  preparing ‘multimedia’:
✔  checking DESCRIPTION meta-information
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘multimedia_0.1.0.tar.gz’

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘brms’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/zc/8vfv33l56bd_3sf0l1g729kr0000gn/T//RtmpVy8q0D/file48845fe2f034/multimedia_0.1.0.tar.gz’ had non-zero exit status
> # install.packages("devtools")
> devtools::install_github("krisrs1128/multimedia")
Downloading GitHub repo krisrs1128/multimedia@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/zc/8vfv33l56bd_3sf0l1g729kr0000gn/T/RtmpVy8q0D/remotes48845859d246/krisrs1128-multimedia-db174e2/DESCRIPTION’ ...
─  preparing ‘multimedia’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘multimedia_0.1.0.tar.gz’

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘brms’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/zc/8vfv33l56bd_3sf0l1g729kr0000gn/T//RtmpVy8q0D/file488470fc1efa/multimedia_0.1.0.tar.gz’ had non-zero exit status
krisrs1128 commented 1 month ago

I apologize for the error! I have pushed a change that I think resolves this error. Could you please let me know if you still see something wrong?

For reference, this happens because we don't want to require installation for some larger packages that are only used in some of the functions. If you try running one of those functions, you should be prompted to install those packages.

krisrs1128 commented 2 days ago

@Ivy-ops Please let us know if you are still running into any difficulties -- in the meantime, I will close this issue. We have been actively revising the package and ended up explicitly importing from all the necessary dependencies. I believe that this resolves all the issues people have encountered with installation, but please let us know if not. Thank you for being interested in the package and sharing your feedback. If there is anything else we can help with, don't hesitate to open a new issue or send an email.