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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Problem in running CreateChromatinAssay() function #195

Closed singcell closed 4 years ago

singcell commented 4 years ago

I have installed the current version of Signac ( Signac_0.2.5) and trying to perform Human PBMCs vignette as practice run. However, when I use function CreateChromatinAssay , I get this message> Error in CreateChromatinAssay() : could not find function "CreateChromatinAssay" I installed using install.packages("Signac") command.

Is it possible that CreateChromatinAssay() to work I need to install Signac 1.0.0.

I get following message, when I attempt to download unreleased development version:

ERROR: dependencies ‘ggbio’, ‘biovizBase’ are not available for package ‘Signac’

PLEASE HELP

sessionInfo:


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_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] Signac_0.2.5

loaded via a namespace (and not attached):
  [1] Seurat_3.2.0           Rtsne_0.15            
  [3] colorspace_1.4-1       deldir_0.1-28         
  [5] ellipsis_0.3.1         ggridges_0.5.2        
  [7] rprojroot_1.3-2        XVector_0.26.0        
  [9] fs_1.5.0               GenomicRanges_1.38.0  
 [11] rstudioapi_0.11        spatstat.data_1.4-3   
 [13] leiden_0.3.3           listenv_0.8.0         
 [15] remotes_2.2.0          ggrepel_0.8.2         
 [17] ggfittext_0.9.0        fansi_0.4.1           
 [19] codetools_0.2-16       splines_3.6.1         
 [21] pkgload_1.1.0          polyclip_1.10-0       
 [23] jsonlite_1.7.0         Rsamtools_2.0.3       
 [25] ica_1.0-2              cluster_2.1.0         
 [27] png_0.1-7              uwot_0.1.8            
 [29] shiny_1.5.0            sctransform_0.2.1     
 [31] compiler_3.6.1         httr_1.4.2            
 [33] backports_1.1.8        assertthat_0.2.1      
 [35] Matrix_1.2-18          fastmap_1.0.1         
 [37] lazyeval_0.2.2         cli_2.0.2             
 [39] later_1.1.0.1          prettyunits_1.1.1     
 [41] htmltools_0.5.0        tools_3.6.1           
 [43] rsvd_1.0.3             igraph_1.2.5          
 [45] gtable_0.3.0           glue_1.4.1            
 [47] GenomeInfoDbData_1.2.2 RANN_2.6.1            
 [49] reshape2_1.4.4         dplyr_1.0.1           
 [51] Rcpp_1.0.5             spatstat_1.64-1       
 [53] vctrs_0.3.2            Biostrings_2.52.0     
 [55] ape_5.4-1              nlme_3.1-148          
 [57] ggseqlogo_0.1          lmtest_0.9-37         
 [59] stringr_1.4.0          ps_1.3.4              
 [61] globals_0.12.5         testthat_2.3.2        
 [63] mime_0.9               miniUI_0.1.1.1        
 [65] lifecycle_0.2.0        irlba_2.3.3           
 [67] devtools_2.3.1         goftest_1.2-2         
 [69] future_1.18.0          MASS_7.3-51.6         
 [71] zlibbioc_1.32.0        zoo_1.8-8             
 [73] scales_1.1.1           promises_1.1.1        
 [75] spatstat.utils_1.17-0  parallel_3.6.1        
 [77] RColorBrewer_1.1-2     gggenes_0.4.0         
 [79] curl_4.3               memoise_1.1.0         
 [81] reticulate_1.16        pbapply_1.4-2         
 [83] gridExtra_2.3          ggplot2_3.3.2         
 [85] rpart_4.1-15           stringi_1.4.6         
 [87] desc_1.2.0             S4Vectors_0.24.4      
 [89] BiocGenerics_0.32.0    pkgbuild_1.1.0        
 [91] BiocParallel_1.20.1    GenomeInfoDb_1.22.1   
 [93] rlang_0.4.7            pkgconfig_2.0.3       
 [95] bitops_1.0-6           lattice_0.20-41       
 [97] ROCR_1.0-11            purrr_0.3.4           
 [99] tensor_1.5             patchwork_1.0.1       
[101] htmlwidgets_1.5.1      processx_3.4.3        
[103] cowplot_1.0.0          tidyselect_1.1.0      
[105] RcppAnnoy_0.0.16       plyr_1.8.6            
[107] magrittr_1.5           R6_2.4.1              
[109] IRanges_2.20.2         generics_0.0.2        
[111] withr_2.2.0            pillar_1.4.6          
[113] mgcv_1.8-31            fitdistrplus_1.1-1    
[115] survival_3.2-3         abind_1.4-5           
[117] RCurl_1.98-1.2         tibble_3.0.3          
[119] future.apply_1.6.0     crayon_1.3.4          
[121] KernSmooth_2.23-17     plotly_4.9.2.1        
[123] usethis_1.6.1          grid_3.6.1            
[125] data.table_1.12.8      callr_3.4.3           
[127] digest_0.6.25          xtable_1.8-4          
[129] tidyr_1.1.1            httpuv_1.5.4          
[131] stats4_3.6.1           munsell_0.5.0         
[133] viridisLite_0.3.0      sessioninfo_1.1.1   ```
timoast commented 4 years ago

You’re looking at the documentation for version 1.0.0 but have version 0.2.5 installed. See the archive page for older versions of the documentation (https://satijalab.org/signac/articles/archive.html) or install the newer version

annpa1231 commented 4 years ago

Hello, I am having difficulty to download signac version 1.0.0

if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager") BiocManager::install() Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Old packages: 'deldir', 'hdf5r', 'Signac' Update all/some/none? [a/s/n]: a

There are binary versions available but the source versions are later: binary source needs_compilation deldir 0.1-28 0.1-29 TRUE hdf5r 1.3.2 1.3.3 TRUE Signac 0.2.5 1.0.0 TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel) no trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/deldir_0.1-28.tgz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/deldir_0.1-28.tgz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/deldir_0.1-28.tgz': HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'deldir' failed trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/hdf5r_1.3.2.tgz' Content type 'application/x-gzip' length 5041178 bytes (4.8 MB)

downloaded 4.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/Signac_0.2.5.tgz' Content type 'application/x-gzip' length 551371 bytes (538 KB)

downloaded 538 KB

The downloaded binary packages are in /var/folders/f7/_h58lt094kv5sn6j93vqb8t40000gp/T//RtmpQn7Uf7/downloaded_packages

Any recommendations? I tried restarting Rstudio but the packages were still not downloaded successfully. Should I just use Signac version 0.2.5?

Thank you