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I just started an intership so i'm not working on my computer. I am trying to update BiocManager to the 3.20 version but without any success no matter what i do the version stays at 3.18 but i can't use it because i have the newest version of R.
I tried what they recommended but it didn't work
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.20")
I don't know if anyone has had the same problem
Please post output from starting R and then running
sessionInfo()(as requested by the web form you use to post questions). I getSorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is coming back today so fingers crossed. I have since been working on a laptop they lent me where i installed R and RStudio. I got a bit distracted.
sessionInfo() R version 4.4.2 (2024-10-31) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 20.04.6 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8
[6] LC_MESSAGES=fr_FR.UTF-8 LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] deldir_2.0-4 pbapply_1.7-0 gridExtra_2.3 rlang_1.1.4 magrittr_2.0.3 RcppAnnoy_0.0.20
[7] matrixStats_0.63.0 ggridges_0.5.4 compiler_4.4.2 spatstat.geom_3.3-5 png_0.1-8 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.0 pkgconfig_2.0.3 fastmap_1.1.0 ellipsis_0.3.2 utf8_1.2.3
[19] promises_1.2.0.1 purrr_1.0.1 jsonlite_1.8.4 goftest_1.2-3 later_1.3.0 spatstat.utils_3.1-2
[25] irlba_2.3.5.1 parallel_4.4.2 cluster_2.1.8 R6_2.5.1 ica_1.0-3 stringi_1.7.12
[31] RColorBrewer_1.1-3 spatstat.data_3.1-4 reticulate_1.40.0 parallelly_1.34.0 spatstat.univar_3.1-1 lmtest_0.9-40
[37] scattermore_1.2 Rcpp_1.0.13-1 tensor_1.5 future.apply_1.10.0 zoo_1.8-11 sctransform_0.4.1
[43] httpuv_1.6.9 Matrix_1.7-2 splines_4.4.2 igraph_2.1.1 tidyselect_1.2.0 abind_1.4-5
[49] spatstat.random_3.3-2 codetools_0.2-19 miniUI_0.1.1.1 spatstat.explore_3.3-4 listenv_0.9.0 lattice_0.22-5
[55] tibble_3.1.8 plyr_1.8.8 shiny_1.7.4 ROCR_1.0-11 Rtsne_0.17 future_1.31.0
[61] fastDummies_1.7.5 survival_3.8-3 polyclip_1.10-4 fitdistrplus_1.1-8 BiocManager_1.30.25 pillar_1.8.1
[67] Seurat_5.2.1 KernSmooth_2.23-26 plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0 sp_1.6-0
[73] ggplot2_3.5.1 munsell_0.5.0 scales_1.3.0 globals_0.16.2 xtable_1.8-4 glue_1.6.2
[79] lazyeval_0.2.2 tools_4.4.2 data.table_1.14.8 RSpectra_0.16-2 RANN_2.6.1 dotCall64_1.2
[85] cowplot_1.1.1 grid_4.4.2 tidyr_1.3.0 colorspace_2.1-0 nlme_3.1-167 patchwork_1.1.2
[91] cli_3.6.0 spatstat.sparse_3.1-0 spam_2.11-1 fansi_1.0.4 viridisLite_0.4.1 dplyr_1.1.0
[97] uwot_0.2.2 gtable_0.3.1 digest_0.6.31 progressr_0.13.0 ggrepel_0.9.3 htmlwidgets_1.6.1
[103] SeuratObject_5.0.2 htmltools_0.5.4 lifecycle_1.0.3 httr_1.4.7 mime_0.12 MASS_7.3-64
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this update? Since 3.20 is the default for R 4.4 you could also try just running
BiocManager::install(); are there any prompts that occur after this? and what you have chosen?Are you sure it stays at 3.18? As in the sessionInfo you did not load BiocManager so we cannot see the result of that? maybe reshare after doing a
library(BiocManager)Could you also share the results of running
R.home()and.libPaths()?Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is coming back today so fingers crossed. I have since been working on a laptop they lent me where i installed R and RStudio. I got a bit distracted.
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8
[6] LC_MESSAGES=fr_FR.UTF-8 LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] deldir_2.0-4 pbapply_1.7-0 gridExtra_2.3 rlang_1.1.4 magrittr_2.0.3 RcppAnnoy_0.0.20
[7] matrixStats_0.63.0 ggridges_0.5.4 compiler_4.4.2 spatstat.geom_3.3-5 png_0.1-8 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.0 pkgconfig_2.0.3 fastmap_1.1.0 ellipsis_0.3.2 utf8_1.2.3
[19] promises_1.2.0.1 purrr_1.0.1 jsonlite_1.8.4 goftest_1.2-3 later_1.3.0 spatstat.utils_3.1-2
[25] irlba_2.3.5.1 parallel_4.4.2 cluster_2.1.8 R6_2.5.1 ica_1.0-3 stringi_1.7.12
[31] RColorBrewer_1.1-3 spatstat.data_3.1-4 reticulate_1.40.0 parallelly_1.34.0 spatstat.univar_3.1-1 lmtest_0.9-40
[37] scattermore_1.2 Rcpp_1.0.13-1 tensor_1.5 future.apply_1.10.0 zoo_1.8-11 sctransform_0.4.1
[43] httpuv_1.6.9 Matrix_1.7-2 splines_4.4.2 igraph_2.1.1 tidyselect_1.2.0 abind_1.4-5
[49] spatstat.random_3.3-2 codetools_0.2-19 miniUI_0.1.1.1 spatstat.explore_3.3-4 listenv_0.9.0 lattice_0.22-5
[55] tibble_3.1.8 plyr_1.8.8 shiny_1.7.4 ROCR_1.0-11 Rtsne_0.17 future_1.31.0
[61] fastDummies_1.7.5 survival_3.8-3 polyclip_1.10-4 fitdistrplus_1.1-8 BiocManager_1.30.25 pillar_1.8.1
[67] Seurat_5.2.1 KernSmooth_2.23-26 plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0 sp_1.6-0
[73] ggplot2_3.5.1 munsell_0.5.0 scales_1.3.0 globals_0.16.2 xtable_1.8-4 glue_1.6.2
[79] lazyeval_0.2.2 tools_4.4.2 data.table_1.14.8 RSpectra_0.16-2 RANN_2.6.1 dotCall64_1.2
[85] cowplot_1.1.1 grid_4.4.2 tidyr_1.3.0 colorspace_2.1-0 nlme_3.1-167 patchwork_1.1.2
[91] cli_3.6.0 spatstat.sparse_3.1-0 spam_2.11-1 fansi_1.0.4 viridisLite_0.4.1 dplyr_1.1.0
[97] uwot_0.2.2 gtable_0.3.1 digest_0.6.31 progressr_0.13.0 ggrepel_0.9.3 htmlwidgets_1.6.1
[103] SeuratObject_5.0.2 htmltools_0.5.4 lifecycle_1.0.3 httr_1.4.7 mime_0.12 MASS_7.3-64
It seems likely this was installed as an admin account and a user account would not be able to update. Someone with admin access should run
BiocManager::install()and choose to update to the latest versions of packages.