BiocManager::install(version = "devel") error

[Roleren]

Starting R from bash:

install.packages("BiocManager")

BiocManager::install(version = "devel")
Error: $ operator is invalid for atomic vectors

BTW: This command works for me on non devel: BiocManager::install("S4Vectors")

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /Home/ii/hakontj/R/x86_64-redhat-linux-gnu-library/R-3.5.1/lib/libRblas.so
LAPACK: /Home/ii/hakontj/R/x86_64-redhat-linux-gnu-library/R-3.5.1/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=nb_NO.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=nb_NO.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=nb_NO.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocManager_1.30.2

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1

[Roleren]

I started Rstudio server, did BiocManager::install(version = "devel"), and then it worked, if I start bash again, it works there too. Strange, but it is fixed at least.

[Roleren]

I tried this on a new computer, now same error in both RStudio and bash, restart did not help. I had to do, BiocManager::install("devel") and not BiocManager::install(version = "devel"). Is this a bug ?

sessionInfo after it worked:

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=nb_NO.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=nb_NO.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=nb_NO.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.2 compiler_3.5.1 tools_3.5.1

[LiNk-NY]

Hi Håkon @Roleren
The first argument for install is packages (pkgs). It shouldn't work like that.

We have a bug fix for this issue in the forthcoming version of BiocManager 1.30.3.
This happens when all packages are up to date (e.g., a clean install). Thanks.

[LiNk-NY]

See #21 for more info.