Problems installing `basilisk` 1.3.6

[csoneson]

I'm having trouble updating basilisk to version 1.3.6 (from 1.3.5, which installed fine), and I was wondering whether any of the recent updates may be the cause for this (or if something may have inadvertently changed on our side). To summarize:

• We're using BASILISK_USE_SYSTEM_DIR=1 (version 1.3.6 installs fine on my laptop where I don't use this)
• The conda directory (inside the basilisk package folder) is correctly detected as the PREFIX when starting the installation, and as the environment location in the package plan.
• However, when it's then trying to activate the environment I get

Preparing transaction: done
Executing transaction: done
installation finished.
sh: /conda/etc/profile.d/conda.sh: No such file or directory
Error in socketAccept(soc, blocking = TRUE, open = "a+b") :
  cannot open the connection
Calls: <Anonymous> ... activateEnvironment -> .activate_condaenv -> socketAccept
In addition: Warning messages:
1: In system(paste(act.cmd, collapse = " "), intern = TRUE) :
  running command '. '/conda/etc/profile.d/conda.sh' && conda activate && /tungstenfs/groups/gbioinfo/Appz/easybuild/software/R/devel-foss-2019b/lib64/R/bin/Rscript --default-packages=NULL -e "con <- socketConnection(port=11121, open='wb', blocking=TRUE);serialize(Sys.getenv(), con);close(con)"' had status 1
2: In socketAccept(soc, blocking = TRUE, open = "a+b") :
  problem in accepting connections on this socket
Execution halted
ERROR: configuration failed for package ‘basilisk’

where it seems that basilisk.utils::getSystemDir() now returns "" rather than the path to the package folder.

Session info

``` R Under development (unstable) (2020-12-05 r79569) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /tungstenfs/groups/gbioinfo/Appz/easybuild/software/OpenBLAS/0.3.7-GCC-8.3.0/lib/libopenblas_skylakex-r0.3.7.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] basilisk.utils_1.3.4 loaded via a namespace (and not attached): [1] BiocManager_1.30.10 compiler_4.1.0 tools_4.1.0 [4] rappdirs_0.3.1 filelock_1.0.2 ```

[LTLA]

Hm. Can you try the latest master of basilisk.utils? I'm pretty sure that's the cause.

[csoneson]

That did not seem to help - same issue after

> BiocManager::install("LTLA/basilisk.utils")
> packageVersion("basilisk.utils")
[1] ‘1.3.5’
> BiocManager::install("basilisk")

(also installing basilisk from GitHub gives the same error).

[LTLA]

Hm. Try again with the latest master (e1e63b6baa719bfa823c6c0b4a82f8edc169e2f8).

[csoneson]

Yep, that seems to have done it. Thanks!