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saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
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Dependencies #43

Closed emily-003 closed 2 years ago

emily-003 commented 2 years ago

Hi- I'm trying to install Liana into R, but I keep getting the message that it can't be installed because I can't install one of the dependencies which is now outdated and doesn't work with the latest version of R. Do you have any suggestions on how to fix this? Many thanks

Warning in install.packages : package ‘RobustRankAggreg’ is not available for this version of R

dbdimitrov commented 2 years ago

Hi @EJCresswell,

Please post your info session.

Daniel

emily-003 commented 2 years ago

R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.utf8

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

other attached packages: [1] extrafont_0.18 readxl_1.4.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[9] tibble_3.1.7 ggplot2_3.3.6 tidyverse_1.3.1 sp_1.5-0 SeuratObject_4.1.0 Seurat_4.1.1

loaded via a namespace (and not attached): [1] backports_1.4.1 plyr_1.8.7 igraph_1.3.2 lazyeval_0.2.2 splines_4.2.1 listenv_0.8.0
[7] scattermore_0.8 usethis_2.1.6 digest_0.6.29 htmltools_0.5.2 fansi_1.0.3 magrittr_2.0.3
[13] memoise_2.0.1 tensor_1.5 cluster_2.1.3 ROCR_1.0-11 tzdb_0.3.0 remotes_2.4.2
[19] globals_0.15.1 modelr_0.1.8 matrixStats_0.62.0 extrafontdb_1.0 spatstat.sparse_2.1-1 prettyunits_1.1.1
[25] colorspace_2.0-3 rvest_1.0.2 ggrepel_0.9.1 haven_2.5.0 callr_3.7.0 crayon_1.5.1
[31] jsonlite_1.8.0 progressr_0.10.1 spatstat.data_2.2-0 survival_3.3-1 zoo_1.8-10 glue_1.6.2
[37] polyclip_1.10-0 gtable_0.3.0 leiden_0.4.2 pkgbuild_1.3.1 Rttf2pt1_1.3.10 future.apply_1.9.0
[43] abind_1.4-5 scales_1.2.0 DBI_1.1.3 spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.8.3
[49] viridisLite_0.4.0 xtable_1.8-4 reticulate_1.25 spatstat.core_2.4-4 htmlwidgets_1.5.4 httr_1.4.3
[55] RColorBrewer_1.1-3 ellipsis_0.3.2 ica_1.0-2 pkgconfig_2.0.3 uwot_0.1.11 dbplyr_2.2.0
[61] deldir_1.0-6 utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.2 reshape2_1.4.4 later_1.3.0
[67] cellranger_1.1.0 munsell_0.5.0 tools_4.2.1 cachem_1.0.6 cli_3.3.0 generics_0.1.2
[73] devtools_2.4.3 broom_0.8.0 ggridges_0.5.3 fastmap_1.1.0 goftest_1.2-3 processx_3.6.1
[79] fs_1.5.2 fitdistrplus_1.1-8 RANN_2.6.1 pbapply_1.5-0 future_1.26.1 nlme_3.1-157
[85] mime_0.12 xml2_1.3.3 rstudioapi_0.13 brio_1.1.3 compiler_4.2.1 curl_4.3.2
[91] plotly_4.10.0 png_0.1-7 testthat_3.1.4 spatstat.utils_2.3-1 reprex_2.0.1 stringi_1.7.6
[97] ps_1.7.1 desc_1.4.1 rgeos_0.5-9 lattice_0.20-45 Matrix_1.4-1 vctrs_0.4.1
[103] pillar_1.7.0 lifecycle_1.0.1 BiocManager_1.30.18 spatstat.geom_2.4-0 lmtest_0.9-40 RcppAnnoy_0.0.19
[109] data.table_1.14.2 cowplot_1.1.1 irlba_2.3.5 httpuv_1.6.5 patchwork_1.1.1 R6_2.5.1
[115] promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3 parallelly_1.32.0 sessioninfo_1.2.2 codetools_0.2-18
[121] MASS_7.3-57 assertthat_0.2.1 pkgload_1.2.4 rprojroot_2.0.3 withr_2.5.0 sctransform_0.3.3
[127] mgcv_1.8-40 parallel_4.2.1 hms_1.1.1 grid_4.2.1 rpart_4.1.16 Rtsne_0.16
[133] shiny_1.7.1 lubridate_1.8.0

dbdimitrov commented 2 years ago

Hi @EJCresswell,

I believe it might be because they removed the package recently from CRAN. https://cran.r-project.org/web/packages/RobustRankAggreg/index.html

Could you try installing it from here: https://cran.r-project.org/src/contrib/Archive/RobustRankAggreg/

I will simply re-implement the algorithm in LIANA's next update and exclude it from the dependencies.

Let me know if that works.

emily-003 commented 2 years ago

Hi- I tried this yesterday and it didn't work. Since updating my R and re-trying today, it seems to have worked ok. Thanks for the help :)

JanLeipzig commented 2 years ago

Hi,

since its a dependency problem as well I will just hijack the issue. I had the same problem with RobustRankAggreg, which I was able to install. But I get an additional error about 'rgeos' after that. The package seems to be still part of CRAN. Any thoughts about that? My R version is 'R version 4.1.3 (2022-03-10) -- "One Push-Up"'

The downloaded source packages are in ‘/tmp/RtmpEExeaQ/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Running R CMD build...

JanLeipzig commented 2 years ago

Actually, installing geos manually fixed the issue for me: 'conda install geos' You probably could include that in your dependencies.

dbdimitrov commented 2 years ago

Hi Jan,

Hmmm, this seems to be more related to conda than liana.

Installing R packages in conda from my experience is always a bit unpredictable and I too often have to manually install certain pacakges.

In other words, don't think that if I include rgeos to liana would solve this, as it already should be imported from SeuratObject or its dependencies.

dbdimitrov commented 2 years ago

I have now re-implemented RRA and the issue should be resolved.

Feel free to re-open in case of any issues.