Error when attempting to install BirdFlowR

[rsmiller74]

When attempting to install BirdFlowR an error is generated for all biconductor dependencies.

Installing 4 packages: Rhdf5lib, S4Vectors, rhdf5filters, rhdf5
Installing packages into ‘C:/Users/apRMiller/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
cannot open URL 'http://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
cannot open URL 'http://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
cannot open URL 'http://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
cannot open URL 'http://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
cannot open URL 'http://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘Rhdf5lib’ ‘S4Vectors’ ‘rhdf5filters’ ‘rhdf5’
These will not be installed
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\apRMiller\AppData\Local\Temp\RtmpcDfsBw\remotesa27c22da74b3\birdflow-science-BirdFlowR-cef92ce/DESCRIPTION' (1.2s)
─ preparing 'BirdFlowR': (11.5s)
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes (1.5s)
-----------------------------------
ERROR: dependency 'rhdf5' is not available for package 'BirdFlowR'
─ removing 'C:/Users/APRMIL~1/AppData/Local/Temp/RtmpgFxa3g/Rinst249474474eca/BirdFlowR'
-----------------------------------
ERROR: package installation failed

[ethanplunkett]

I'll see if I can figure out what's going on. In the meantime @rsmiller74 see if you can install rhdf5 manually. I'd try this first:

devtools::install_bioc("rhdf5")

If that doesn't work try using the bioconductor installer to install rhdf5 although it has a tendency to install a ton of packages.

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("rhdf5")

And then try installing BirdFlowR again.

[rsmiller74]

I was able to install the problematic Bioconducter packages using BiocManager. Then when Attempting to install BirdFlowR using

remotes::install_github("birdflow-science/BirdFlowR", build_vignettes = TRUE)

It then failed on lines 26-30 [setup] (Preprocess.Rmd) due to no ebirdst package.

Quitting from lines 26-30 [setup] (Preprocess.Rmd)
Error: processing vignette 'Preprocess.Rmd' failed with diagnostics:
there is no package called 'ebirdst'
--- failed re-building 'Preprocess.Rmd'

SUMMARY: processing the following file failed:
'Preprocess.Rmd'

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'BirdFlowR' from GitHub:
! System command 'Rcmd.exe' failed

I then installed ebirdst from CRAN. Rerunning remotes::install_github() appears to run correctly with a valid installation of BirdFlowR.

[ethanplunkett]

I'm sorry it was so convoluted. Thanks for reporting!

[ethanplunkett]

To fix this:

• Add a note to the main readme suggesting that bioconductor packages might have to be installed manually. Copy instructions from above.
• Either:
  • Move ebirdst from suggests to imports so it is installed when BirdFlowR is installed.
  • Update readme to install all the suggested packages if building vignettes. Use dependencies = TRUE when calling devtools::install_git()