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gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
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FRASER 2.0 versions not available #87

Open Wynandi opened 4 weeks ago

Wynandi commented 4 weeks ago

Hello,

I am trying to update to a FRASER package which corresponds to FRASER 2.0. According to GitHub anything above 1.9 would do and an R version of 4.0.0 or higher should enable installation with BiocManager.

Unfortunately, I am unable to install any version above 1.14.1.

available.packages(repos=BiocManager::repositories())["FRASER", "Version"] [1] "1.14.1" R.version _ platform x86_64-conda-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 4 minor 3.3 year 2024 month 02 day 29 svn rev 86002 language R version.string R version 4.3.3 (2024-02-29) nickname Angel Food Cake packageDescription("FRASER")$Version [1] "1.14.1" BiocManager::install("FRASER") Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29) Old packages: 'BiocFileCache', 'broom', 'bslib', 'cachem', 'curl', 'data.table', 'DBI', 'dbplyr', 'evaluate', 'farver', 'fastmap', 'fs', 'future', 'future.apply', 'GenomeInfoDb', 'ggplot2', 'gtable', 'hardhat', 'highr', 'htmltools', 'httpuv', 'KernSmooth', 'knitr', 'lattice', 'matrixStats', 'munsell', 'nlme', 'openssl', 'promises', 'ragg', 'RcppArmadillo', 'repr', 'rlang', 'rmarkdown', 'RSQLite', 'rstudioapi', 'seriation', 'shiny', 'stringi', 'survival', 'systemfonts', 'textshaping', 'tinytex', 'vegan', 'VGAM', 'xfun', 'xts' Update all/some/none? [a/s/n]: n Warning message: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'FRASER'

I tried the force installation or updating other packages but ended up with the same FRASER version.

AtaJadidAhari commented 4 weeks ago

Hi, can you please try to install the latest release from github? devtools::install_github('gagneurlab/FRASER', ref='1.99.4', dependencies=TRUE) Should do the trick.

As to why installing from Bioconductor fails: FRASER 2.0.0 is available on Bioconductor release of 3.19. I suspect that you are trying to install with a previous Bioconductor release (3.18) and that's why you end up installing 1.14.1.

AtaJadidAhari commented 4 weeks ago

@vyepez88 @ischeller should we update the readme to propose installing from github as default?