Issue with GitHub install of CompoundDb

[redbluewater]

I am excited to try the new options presented in your 2022 Metabolites paper, but I have run into an issue with installing CompoundDb (and perhaps others). I originally started with the option in the paper to install the full tutorial :

install.packages("BiocManager")
BiocManager::install("jorainer/MetaboAnnotationTutorials")

But when it complained about not installing CompoundDb, I tried that directly:

install.packages(c("BiocManager", "remotes"))
BiocManager::install("RforMassSpectrometry/CompoundDb")

Then I get the following:

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing github package(s) 'RforMassSpectrometry/CompoundDb'
Downloading GitHub repo RforMassSpectrometry/CompoundDb@HEAD
√  checking for file 'C:\Users\xxxx\AppData\Local\Temp\RtmpKK9xNo\remotes1208858704824\rformassspectrometry-CompoundDb-2453c53/DESCRIPTION' (537ms)
-  preparing 'CompoundDb': (458ms)
√  checking DESCRIPTION meta-information ...
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'CompoundDb_0.99.9.tar.gz'
   
* installing *source* package 'CompoundDb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: class "MsBackendCached" is not exported by 'namespace:Spectra'
Execution halted
ERROR: lazy loading failed for package 'CompoundDb'
* removing 'C:/Users/xxx/Documents/R/win-library/4.1/CompoundDb'
installation of package �C:/Users/xxx/AppData/Local/Temp/RtmpKK9xNo/file12088555b43b5/CompoundDb_0.99.9.tar.gz� had non-zero exit status

Any thoughts? I would really like to try this out, but I am stumped (and my R troubleshooting skills are not the best). And my sessionInfo() follows

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] prettyunits_1.1.1   ps_1.6.0            withr_2.5.0         rprojroot_2.0.2     crayon_1.5.0       
 [6] digest_0.6.29       R6_2.5.1            evaluate_0.15       rlang_1.0.2         cli_3.2.0          
[11] curl_4.3.2          rstudioapi_0.13     remotes_2.4.2       callr_3.7.0         rmarkdown_2.13     
[16] tools_4.1.3         tinytex_0.37        processx_3.5.2      xfun_0.30           yaml_2.3.5         
[21] fastmap_1.1.0       compiler_4.1.3      pkgbuild_1.3.1      BiocManager_1.30.16 htmltools_0.5.2    
[26] knitr_1.37 

[jorainer]

Really sorry about these installation problems! We made some quite drastic changes recently, thus all packages need to be the most recent developmental versions. All problems should however go away with the upcoming Bioconductor release.

I guess the installed Spectra package must be too old. Actually, the BiocManager::install("jorainer/MetaboAnnotationTutorials") call should have installed/updated all packages properly, but I guess something must have gone wrong.

Please try the following:

BiocManager::install("RforMassSpectrometry/ProtGenerics")
BiocManager::install("RforMassSpectrometry/MsCoreUtils")
BiocManager::install("RforMassSpectrometry/Spectra")
BiocManager::install("RforMassSpectrometry/MetaboCoreUtils")
BiocManager::install("RforMassSpectrometry/CompoundDb")

Installing the packages in that order should fix the installation problems. Please let me know if it's still not working.

[redbluewater]

Excellent - this works just fine. Thanks for the update and added help. I appreciate it, and I look forward to using this package. Cheers.

[jorainer]

Great! I'm closing the issue now. Feel free to re-open. And also please let me know if you run into problems or see features/things that could be improved!