FRASER 2.0 versions not available

[Wynandi]

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]

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]

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