Hi, I am just posting what Travis CI output is showing for R-devel. It seems that there are some packages which have newer versions and these are installed. This was not happening in May.

$ Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'
BiocGenerics (0.35.2  -> 0.35.4 ) [CRAN]
rmarkdown    (2.1     -> 2.2    ) [CRAN]
mvtnorm      (1.1-0   -> 1.1-1  ) [CRAN]
htmltools    (0.4.0   -> 0.5.0  ) [CRAN]
httpuv       (1.5.3.1 -> 1.5.4  ) [CRAN]
later        (1.0.0   -> 1.1.0.1) [CRAN]
promises     (1.1.0   -> 1.1.1  ) [CRAN]
vctrs        (0.3.0   -> 0.3.1  ) [CRAN]
pkgload      (1.0.2   -> 1.1.0  ) [CRAN]

Now during the install process of BiocGeneric I can see the which.min and which.max function being set as new generic functions. However, the which function is not among them. Might this be the problem of the initial issue "Warning: multiple methods tables found for 'which'"?

* installing *source* package ‘BiocGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
Creating a new generic function for ‘get’ in package ‘BiocGenerics’
Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘match’ in package ‘BiocGenerics’
Creating a new generic function for ‘order’ in package ‘BiocGenerics’
Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
Creating a new generic function for ‘union’ in package ‘BiocGenerics’
Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
Creating a new generic function for ‘table’ in package ‘BiocGenerics’
Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
Creating a new generic function for ‘var’ in package ‘BiocGenerics’
Creating a new generic function for ‘sd’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
...

Hi,

as fas as I understood R-devel is for testing, if everything compiles and to find bugs in future versions.

I will attach the travis.yml file and try to add the installation of the latest package versions. Maybe you can give a hint how to do that efficiently.

Thank you in anticipation

Best regards

Kristian

language: r cache: packages warningsareerrors: true biocrequired: true biocpackages: - Biostrings os: linux dist: bionic beforeinstall: - sudo apt-get update - sudo apt-get -y install libcurl4-openssl-dev libssl-dev libxml2-dev pandoc libglu1-mesa-dev rpackages: - devtools - testthat - seqinr - foreach - doMC - magrittr - mclust - feature r: - release - devel