Question: Updating package CATALYST
0
gravatar for Brent.OCarrigan
21 days ago by
Brent.OCarrigan0 wrote:

Hi Mark & Helena,

Having difficulty updating to the latest version of CATALYST (1.10) on my local Mac, worked fine on a remote cluster. - Current R (3.6.1), current Bioconductor v 3.9, current BiocManager v1.3.10

Installation still pulls in the previous CATALYST v1.87

> BiocManager::install("CATALYST")
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'CATALYST'
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/CATALYST_1.8.7.tgz'
Content type 'application/x-gzip' length 9235873 bytes (8.8 MB)
==================================================
downloaded 8.8 MB


The downloaded binary packages are in
    /var/folders/kp/dwz7y9gx6n37wt0f12yp8x2s8cbn2c/T//RtmpC3Zbxy/downloaded_packages
Old packages: 'roxygen2', 'VGAM'
Update all/some/none? [a/s/n]: 
n

Even if I restart R + Rstudio, then repeat specifying update = TRUE

> BiocManager::install("CATALYST", update = TRUE)
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'CATALYST'
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/CATALYST_1.8.7.tgz'
Content type 'application/x-gzip' length 9235873 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

Then restart R + Rstudio and install from source: still the previous CATALYST v1.87

> BiocManager::install("CATALYST", type = 'source', update = TRUE)
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'CATALYST'
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/CATALYST_1.8.7.tar.gz'
Content type 'application/x-gzip' length 7811312 bytes (7.4 MB)
==================================================
downloaded 7.4 MB

* installing *source* package ‘CATALYST’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘filter’ in package ‘CATALYST’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CATALYST)

Any thoughts?

> sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] CATALYST_1.8.7

loaded via a namespace (and not attached):
  [1] ggbeeswarm_0.6.0            TH.data_1.0-10              Rtsne_0.15                 
  [4] colorspace_1.4-1            rjson_0.2.20                rio_0.5.16                 
  [7] ggridges_0.5.1              circlize_0.4.8              corpcor_1.6.9              
 [10] XVector_0.24.0              BiocNeighbors_1.2.0         GenomicRanges_1.36.1       
 [13] GlobalOptions_0.1.1         clue_0.3-57                 rstudioapi_0.10            
 [16] ggrepel_0.8.1               DT_0.10                     mvtnorm_1.0-11             
 [19] codetools_0.2-16            splines_3.6.1               robustbase_0.93-5          
 [22] scater_1.12.2               zeallot_0.1.0               jsonlite_1.6               
 [25] cluster_2.1.0               png_0.1-7                   shinydashboard_0.7.1       
 [28] graph_1.62.0                shiny_1.4.0                 BiocManager_1.30.10        
 [31] rrcov_1.4-7                 compiler_3.6.1              httr_1.4.1                 
 [34] drc_3.0-1                   backports_1.1.5             fastmap_1.0.1              
 [37] assertthat_0.2.1            Matrix_1.2-17               lazyeval_0.2.2             
 [40] limma_3.40.6                BiocSingular_1.0.0          later_1.0.0                
 [43] htmltools_0.4.0             tools_3.6.1                 rsvd_1.0.2                 
 [46] igraph_1.2.4.1              gtable_0.3.0                glue_1.3.1                 
 [49] GenomeInfoDbData_1.2.1      reshape2_1.4.3              dplyr_0.8.3                
 [52] Rcpp_1.0.3                  carData_3.0-3               Biobase_2.44.0             
 [55] cellranger_1.1.0            vctrs_0.2.0                 DelayedMatrixStats_1.6.1   
 [58] stringr_1.4.0               openxlsx_4.1.3              mime_0.7                   
 [61] irlba_2.3.3                 lifecycle_0.1.0             gtools_3.8.1               
 [64] XML_3.98-1.20               DEoptimR_1.0-8              zlibbioc_1.30.0            
 [67] MASS_7.3-51.4               zoo_1.8-6                   scales_1.1.0               
 [70] shinyBS_0.61                hms_0.5.2                   promises_1.1.0             
 [73] parallel_3.6.1              SummarizedExperiment_1.14.1 sandwich_2.5-1             
 [76] RColorBrewer_1.1-2          SingleCellExperiment_1.6.0  ComplexHeatmap_2.0.0       
 [79] curl_4.2                    gridExtra_2.3               ggplot2_3.2.1              
 [82] stringi_1.4.3               S4Vectors_0.22.1            pcaPP_1.9-73               
 [85] plotrix_3.7-6               flowCore_1.50.0             BiocGenerics_0.30.0        
 [88] zip_2.0.4                   BiocParallel_1.18.1         shape_1.4.4                
 [91] GenomeInfoDb_1.20.0         rlang_0.4.1                 pkgconfig_2.0.3            
 [94] matrixStats_0.55.0          bitops_1.0-6                lattice_0.20-38            
 [97] purrr_0.3.3                 htmlwidgets_1.5.1           tidyselect_0.2.5           
[100] plyr_1.8.4                  magrittr_1.5                R6_2.4.1                   
[103] IRanges_2.18.3              nnls_1.4                    multcomp_1.4-10            
[106] DelayedArray_0.10.0         pillar_1.4.2                haven_2.2.0                
[109] foreign_0.8-72              survival_3.1-7              abind_1.4-5                
[112] RCurl_1.95-4.12             FlowSOM_1.16.0              tibble_2.1.3               
[115] tsne_0.1-3                  crayon_1.3.4                car_3.0-5                  
[118] plotly_4.9.1                viridis_0.5.1               GetoptLong_0.1.7           
[121] grid_3.6.1                  readxl_1.3.1                data.table_1.12.6          
[124] ConsensusClusterPlus_1.48.0 forcats_0.4.0               digest_0.6.22              
[127] xtable_1.8-4                httpuv_1.5.2                tidyr_1.0.0                
[130] stats4_3.6.1                munsell_0.5.0               beeswarm_0.2.3             
[133] viridisLite_0.3.0           vipor_0.4.5                 shinyjs_1.0                
cytofworkflow catalyst • 113 views
ADD COMMENTlink modified 21 days ago by Martin Morgan ♦♦ 24k • written 21 days ago by Brent.OCarrigan0
Answer: Updating package CATALYST
2
gravatar for Martin Morgan
21 days ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Update the version of Bioconductor you're using

BiocManager::install(version="3.10")

and try again. Note that this will ask to update (and you should) all Bioconductor packages. If it's important to retain your current installation, e.g., for reproducibility, then consider following the discussion in vignette(package="BiocManager", "BiocManager") section "managing multiple versions".

ADD COMMENTlink written 21 days ago by Martin Morgan ♦♦ 24k

Thanks Martin! All fixed. I thought I was current with (BiocManager 1.30.10) but had missed the version 3.9 number.

ADD REPLYlink written 20 days ago by Brent.OCarrigan0
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