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Installation issues with R 3.5+ ? #3

Open gal-lum opened 3 years ago

gal-lum commented 3 years ago

Hi shmooTL devs,

I'm trying to follow the installation guide (through RStudio, R version 4.1) and running into an issue with this line: source('https://bioconductor.org/biocLite.R')

I'm getting the following error:

Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

If I do use BiocManager as they suggest:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install('VariantAnnotation') BiocManager::install('rhdf5')

then when I later get to installing shmooTL, it doesn't recognize that they were installed:

install_github('gact/shmootl', build_vignettes=TRUE) Downloading GitHub repo gact/shmootl@HEAD Skipping 8 packages not available: VariantAnnotation, S4Vectors, rtracklayer, rhdf5, IRanges, GenomicRanges, GenomeInfoDb, BiocGenerics

and installation fails with:

ERROR: package installation failed Error: Failed to install 'shmootl' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines): E> ** data E> * moving datasets to lazyload DB E> inst E> * byte-compile and prepare package for lazy loading E> Error: object 'h5writeAttribute.array' is not exported by 'namespace:rhdf5' E> Execution halted E> ERROR: lazy loading failed for package 'shmootl' E> removing 'C:/Users//AppData/Local/Temp/RtmpIdMB6V/Rinst125c74a3185a/shmootl' E> ----------------------------------- E> ERROR: package installation failed

Is there a way to solve this? Am I doing something wrong? Should I be using an earlier version of R?

tw164 commented 3 years ago

Hi @gal-lum,

The ShmooTL package is not yet available for R version 4. Would it be acceptable to use R version 3 in the meantime?

It should be possible to install on R version 3.6, for example, though you may need to set build_vignettes to FALSE to avoid the warning about the Bioconductor packages.

The Bioconductor installation info in the package README was admittedly out of date, so I’ve updated and simplified it.

gal-lum commented 3 years ago

Hi,

thanks for replying. I wouldn't mind an earlier R version, but having the vignettes might be nice. What would be the recommended R version to run this package in? 3.0?

tw164 commented 3 years ago

If you have complete freedom regarding which version of R to use, I'd recommend R version 3.0.2 as that is the version of R for which the package was developed.

Regarding the vignettes, it actually seems to build these OK if build_vignettes is set to TRUE, despite the warnings about the Bioconductor packages. Of course, for installing ShmooTL itself, the Bioconductor packages VariantAnnotation, rhdf5 and rmarkdown still need to be installed separately using BiocManager (as you've described) prior to installing ShmooTL.