Updating package CATALYST
1
0
Entering edit mode
@brentocarrigan-21529
Last seen 3.2 years ago

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                
CATALYST cytofWorkflow • 892 views
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2
Entering edit mode
@martin-morgan-1513
Last seen 3 days ago
United States

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".

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0
Entering edit mode

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

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