Make a new Bioconductor release

[danielinteractive]

Quite long since we did the BioC release.

Also we got this message on 11 Jan:

We would like to bring to your attention that your package is failing in devel across all platforms. This is very problematic. Please investigate the issues and fix the package to avoid deprecation.

https://bioconductor.org/checkResults/devel/bioc-LATEST/

If you have further questions or concerns please reach out on the bioc-devel@r-project.org

Error is occurring during byte-compilation:

* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘hermes’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error : in method for ‘counts<-’ with signature ‘object="AnyHermesData",value="matrix"’:  arguments (‘value’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list
Error: unable to load R code in package ‘hermes’
Execution halted
ERROR: lazy loading failed for package ‘hermes’
* removing ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/hermes’

https://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc has tips for reproducing this.

Let's use the Docker container:

docker run \
        --mount type=bind,source=/Users/sabanesd/git,target=/git \
        -e ROOT=true \
        -e PASSWORD=bioc \
        -p 8787:8787 \
        bioconductor/bioconductor_docker:devel

Then in the web browser open http://localhost:8787 and enter user name rstudio and password bioc.
Then open -> /git/hermes project

install.packages("remotes")
remotes::install_github("cran4linux/rspm")

In the terminal:

sudo apt-get update
sudo apt -y install apt-file

Back in R:

rspm::install_sysreqs()
rspm::enable()
install.packages("devtools")
rspm::disable() # because above fails at Rcpp
install.packages("devtools")
devtools::install_dev_deps() # takes quite a while

In terminal:

cd ..
git clone https://github.com/bioconductor/S4Arrays
R CMD INSTALL S4Arrays
git clone https://github.com/bioconductor/SparseArray
R CMD INSTALL SparseArray

Back in R:

devtools::install_dev_deps()

Then "Install and Restart" gives the error

• first: fix this on IE GH
• second: merge main IE into devel BioC, see https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel - check again https://bioconductor.org/checkResults/devel/bioc-LATEST/hermes/ to see status

[danielinteractive]

Hit the problem that I cannot install the dependency S4Arrays because the compilation fails with

array_selection.c: In function ‘C_Lindex2Mindex’:
array_selection.c:352:17: error: format not a string literal and no format arguments [-Werror=format-security]
  352 |                 error(errmsg_buf());
      |                 ^~~~~
array_selection.c: In function ‘C_Mindex2Lindex’:
array_selection.c:416:17: error: format not a string literal and no format arguments [-Werror=format-security]
  416 |                 error(errmsg_buf());
      |                 ^~~~~
cc1: some warnings being treated as errors

Am I doing something wrong maybe? I expected that S4Arrays should install just fine because
https://bioconductor.org/checkResults/devel/bioc-LATEST/S4Arrays/
shows that its checks on BioC devel pass, and I assumed that the same Docker image is used?

Revisit https://stat.ethz.ch/pipermail/bioc-devel/2024-January/thread.html to see any responses to my question

[danielinteractive]

Have merged main into devel via branch https://github.com/insightsengineering/hermes/tree/update_from_ie

[danielinteractive]

It is all green on BioC:
https://bioconductor.org/checkResults/devel/bioc-LATEST/hermes/