Unable to install liana on R

[SNayabFA]

Hello

I have been trying to install liana but keep running into the error below:

Error in pkgdesc$Version : $ operator is invalid for atomic vectors
In addition: Warning message:
In utils::packageDescription(pkg, fields = c("Package", "Version")) :
no package 'crancache' was found
Installing package into ‘/mnt/user-library/r440-bioc319-20231108’
(as ‘lib’ is unspecified)

• installing source package ‘liana’ ...
  ** using staged installation
  Error: 'installMiniconda' is not an exported object from 'namespace:basilisk.utils'
  Execution halted
  Error in file(filename, "r") : cannot open the connection
  Calls: -> eval -> parse -> file
  In addition: Warning message:
  In file(filename, "r") :
  cannot open file 'R/basilisk.R': No such file or directory
  Execution halted
  ERROR: configuration failed for package ‘liana’
• removing ‘/mnt/user-library/r440-bioc319-20231108/liana’
  Warning message:
  In i.p(...) :
  installation of package ‘/local/tmp/Rtmphzb8RX/filef26729ead/liana_0.1.14.tar.gz’ had non-zero exit status

R Under development (unstable) (2023-12-04 r85659)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.11.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] remotes_2.5.0 basilisk.utils_1.17.2 basilisk_1.17.2 reticulate_1.38.0
[5] BiocManager_1.30.23 magrittr_2.0.3 lubridate_1.9.3 forcats_1.0.0
[9] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[13] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0

loaded via a namespace (and not attached):
[1] dir.expiry_1.13.0 gtable_0.3.5 htmlwidgets_1.6.4 devtools_2.4.5 processx_3.8.4
[6] lattice_0.22-6 callr_3.7.6 tzdb_0.4.0 ps_1.7.6 vctrs_0.6.5
[11] tools_4.4.0 generics_0.1.3 curl_5.2.2 parallel_4.4.0 fansi_1.0.6
[16] pkgconfig_2.0.3 Matrix_1.6-4 desc_1.4.3 lifecycle_1.0.4 compiler_4.4.0
[21] munsell_0.5.1 codetools_0.2-20 httpuv_1.6.15 htmltools_0.5.8.1 usethis_2.2.3
[26] later_1.3.2 pillar_1.9.0 urlchecker_1.0.1 ellipsis_0.3.2 cachem_1.1.0
[31] sessioninfo_1.2.2 mime_0.12 parallelly_1.38.0 tidyselect_1.2.1 digest_0.6.37
[36] stringi_1.8.4 future_1.34.0 reshape2_1.4.4 listenv_0.9.1 fastmap_1.2.0
[41] grid_4.4.0 colorspace_2.1-1 cli_3.6.3 pkgbuild_1.4.4 utf8_1.2.4
[46] withr_3.0.1 filelock_1.0.3 scales_1.3.0 promises_1.3.0 timechange_0.3.0
[51] globals_0.16.3 png_0.1-8 hms_1.1.3 memoise_2.0.1 shiny_1.8.1.1
[56] miniUI_0.1.1.1 profvis_0.3.8 rlang_1.1.4 Rcpp_1.0.13 xtable_1.8-4
[61] glue_1.7.0 pkgload_1.3.4 jsonlite_1.8.8 rstudioapi_0.16.0 R6_2.5.1
[66] plyr_1.8.9 fs_1.6.4

[deeenes]

Try install from this PR

remotes::install_github('saezlab/liana#172')

[SNayabFA]

Still getting this error. I think my organization is unable to use miniconda (which is what the error keeps bringing up). Any way to use miniforge instead?

Error in pkgdesc$Version : $ operator is invalid for atomic vectors
In addition: Warning messages:
1: In i.p(...) :
installation of package ‘SeuratObject’ had non-zero exit status
2: In utils::packageDescription(pkg, fields = c("Package", "Version")) :
no package 'crancache' was found
Installing package into ‘/mnt/user-library/r421-bioc316-20221122’
(as ‘lib’ is unspecified)

• installing source package ‘liana’ ...
  ** using staged installation
  Error: 'installMiniconda' is not an exported object from 'namespace:basilisk.utils'
  Execution halted
  Error in file(filename, "r") : cannot open the connection
  Calls: -> eval -> parse -> file
  In addition: Warning message:
  In file(filename, "r") :
  cannot open file 'R/basilisk.R': No such file or directory
  Execution halted
  ERROR: configuration failed for package ‘liana’
• removing ‘/mnt/user-library/r421-bioc316-20221122/liana’
  Warning message:
  In i.p(...) :
  installation of package ‘/local/tmp/Rtmpwsk102/file59f27993b91/liana_0.1.14.tar.gz’ had non-zero exit status