package ‘recount’ is not available for Bioconductor version '3.19'
Closed this issue · 5 comments
Hello,
Thanks in advance!
I'm having issues trying to install recount in R (Ubuntu 22.04 host) that I've not experienced before. Below is the terminal output and session info;
> if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 (2024-04-24)
> BiocManager::install("recount")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 (2024-04-24)
Installing package(s) 'recount'
Warning message:
package ‘recount’ is not available for Bioconductor version '3.19'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
time zone: Australia/Adelaide
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.22
loaded via a namespace (and not attached):
[1] compiler_4.4.0 tools_4.4.0
Package recount3 installs without issues as do many other packages however I still require recount.
As can be seen in the error, it has to do with the very recent release of the latest version of R and BiocManager.
I am looking for any ideas about how I can overcome this incompatibility issue?
Hullo, reporting basically the same issue of @twobeers75
Recount3 installs without any issues for me as well.
I'll try doing some tests with older versions of R and BiocManager. If someone has any ideas I'll try to implement the and report results
> BiocManager::install('recount')
'getOption("repos")' replaces Bioconductor standard repositories,
see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0
(2024-04-24)
Installing package(s) 'recount'
Messaggio di avvertimento:
il pacchetto ‘recount’ non è disponibile for this version of R
Una versione di questo pacchetto per la tua versione di R potrebbe essere disponibile altrove,
si veda su
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: ArcoLinux
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblas.so.0.3; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Rome
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.4.0 tools_4.4.0
OK recount seems to work with R versions >=4.1 but <4.4 obviously. To install several R versions I decided to use virtual environments: I used micromamba but using mamba or conda should give the same results.
A wierd thing that happens is that it requires to install R package XML (or maybe library libxml2) through micromamba/mamba/conda. After some testing I decided to go for the 4.3 version.
micromamba env create -n R-4-3-recount r-base=4.3 r-recommended r-xml
micromamba activate R-4-3-recount
# just to make sure we're using the correct R binary inside the virtual environment and the correct version
which R
R --version
# now run R
RNow in R:
install.packages('BiocManager')
BiocManager::install('recount')Note: if you're using RStudio, run RStudio from terminal after activating the virtual environment.
@twobeers75 let me know if it works for you!
Brilliant! I did not think this would work for my situation but I can confirm that it does.
Thank you @MorfeoRenai, good enough work around for now. My code below;
I used Anaconda,
conda create -n r_env r-essentials r-base=4.3 r-recommended r-xml
conda activate r_env
then in R
R
>if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install('recount')
Works like a charm! Thanks again.
Hi,
From https://bioconductor.org/packages/release/bioc/html/recount.html I do see the landing page for recount on BioC 3.19. Though there are some build errors in operating systems except for winOS https://bioconductor.org/checkResults/release/bioc-LATEST/recount/
This is is most likely related to issues with rtracklayer::import.bw() related to lawremi/rtracklayer#73 and lawremi/rtracklayer#83.
Best,
Leo
Hi,
I posted an update at lawremi/rtracklayer#83 (comment) and also edited the recount vignette to implement a workaround to the rtracklayer::import() issues for remote BigWig files. The workaround involves downloading the data first.
Given the results at https://github.com/leekgroup/recount/actions/runs/9178757128, I anticipate that recount3 will become available on bioc 3.19 and 3.20 on all platforms in 24-48 hrs.
I'll go ahead and close this issue in the meantime, but feel free to re-open it after 48 hrs if the issue persists.
Best,
Leo