Question: Seurat 2.3.4 installation
0
gravatar for Mike
7 months ago by
Mike10
Mike10 wrote:

I tried many times to reinstall the previous version of Seurat (2.3.4) using following command

install.packages('Seurat', repo = c('satijalab.org/ran/' getOption("repos")))

but after installation, it keeps loading the newest version of Seurat (3.0.0).

Could you tell me why and how I can reinstall the older version?

Here is my sessionInfo()

R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Seurat_3.0.0                MultiAssayExperiment_1.8.3  SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.6         matrixStats_0.54.0         
 [7] Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.2         IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
 [1] tsne_0.1-3             nlme_3.1-139           bitops_1.0-6           httr_1.4.0             RColorBrewer_1.1-2     rstan_2.18.2           sctransform_0.2.0     
 [8] tools_3.5.3            R6_2.4.0               irlba_2.3.3            KernSmooth_2.23-15     lazyeval_0.2.2         colorspace_1.4-1       npsurv_0.4-0          
[15] tidyselect_0.2.5       gridExtra_2.3          prettyunits_1.0.2      processx_3.3.0         compiler_3.5.3         cli_1.1.0              plotly_4.9.0          
[22] caTools_1.17.1.2       scales_1.0.0           lmtest_0.9-36          pbapply_1.4-0          ggridges_0.5.1         callr_3.2.0            stringr_1.4.0         
[29] digest_0.6.18          StanHeaders_2.18.1     R.utils_2.8.0          XVector_0.22.0         htmltools_0.3.6        pkgconfig_2.0.2        bibtex_0.4.2          
[36] htmlwidgets_1.3        rlang_0.3.4            rstudioapi_0.10        jsonlite_1.6           zoo_1.8-5              ica_1.0-2              gtools_3.8.1          
[43] dplyr_0.8.0.1          R.oo_1.22.0            inline_0.3.15          RCurl_1.95-4.12        magrittr_1.5           GenomeInfoDbData_1.2.0 loo_2.1.0             
[50] Matrix_1.2-17          Rcpp_1.0.1             munsell_0.5.0          reticulate_1.12        ape_5.3                R.methodsS3_1.7.1      stringi_1.4.3         
[57] gbRd_0.4-11            MASS_7.3-51.3          zlibbioc_1.28.0        pkgbuild_1.0.3         gplots_3.0.1.1         Rtsne_0.15             plyr_1.8.4            
[64] grid_3.5.3             gdata_2.18.0           listenv_0.7.0          ggrepel_0.8.0          crayon_1.3.4           lattice_0.20-38        cowplot_0.9.4         
[71] splines_3.5.3          SDMTools_1.1-221.1     ps_1.3.0               pillar_1.3.1           igraph_1.2.4.1         reshape2_1.4.3         future.apply_1.2.0    
[78] codetools_0.2-16       glue_1.3.1             lsei_1.2-0             metap_1.1              data.table_1.12.2      png_0.1-7              Rdpack_0.11-0         
[85] tidyr_0.8.3            gtable_0.3.0           RANN_2.6.1             purrr_0.3.2            future_1.12.0          assertthat_0.2.1       ggplot2_3.1.1         
[92] rsvd_1.0.0             viridisLite_0.3.0      survival_2.44-1.1      tibble_2.1.1           cluster_2.0.8          globals_0.12.4         fitdistrplus_1.0-14   
[99] ROCR_1.0-7 
seurat • 751 views
ADD COMMENTlink modified 7 months ago by Gordon Smyth39k • written 7 months ago by Mike10

Hi you could also install directly from github. However first you need to remove.packages("Seurat") then make sure that you have

install.packages("devtools")
library(devtools);
devtools::install_github(repo = 'satijalab/seurat', ref = 'release/2.4', dependencies=T)

make sure to restart R in between.

ADD REPLYlink written 7 months ago by Ahdee40
Answer: Seurat 2.3.4 installation
1
gravatar for Aaron Lun
7 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

Seurat is not a Bioconductor package, so this is not the right forum for such questions. You would be better served by asking R-help... or, in fact, Dr. Google, who would quickly point you to https://cran.r-project.org/src/contrib/Archive/.

ADD COMMENTlink written 7 months ago by Aaron Lun25k

Asking R-help for guidance about how to get old versions of CRAN packages should be ok, but don't ask Seurat-specific questions on R-help. The R-help posting guide says:

If the question relates to a contributed package , e.g., one downloaded from CRAN, try contacting the package maintainer first. ... Only send such questions to R-help or R-devel if you get no reply or need further assistance. This applies to both requests for help and to bug reports.

ADD REPLYlink written 6 months ago by Gordon Smyth39k
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