Can't install the ArchR on MacOS 15.0.1 #2221

penghy27 · 2024-10-20T22:56:34Z

Describe the bug

I followed suggestions from previous posts to revert to an older R version (e.g. 4.1.3) because ArchR would not install with the updated R 4.4. However, I still can't install ArchR. I still receive the same following error even after running install.packages("usethis")

> devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘usethis’

Any suggestions I can check my system or any settings?

Session Info

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 15.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
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   base     

other attached packages:
[1] Matrix_1.4-0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.13         compiler_4.1.3      later_1.3.2        
 [4] BiocManager_1.30.25 urlchecker_1.0.1    profvis_0.4.0      
 [7] remotes_2.5.0       tools_4.1.3         digest_0.6.37      
[10] pkgbuild_1.4.4      pkgload_1.4.0       evaluate_1.0.1     
[13] memoise_2.0.1       lifecycle_1.0.4     lattice_0.22-6     
[16] rlang_1.1.4         shiny_1.9.1         cli_3.6.3          
[19] rstudioapi_0.17.0   yaml_2.3.10         xfun_0.48          
[22] fastmap_1.2.0       knitr_1.48          fs_1.6.4           
[25] htmlwidgets_1.6.4   grid_4.1.3          R6_2.5.1           
[28] rmarkdown_2.28      sessioninfo_1.2.2   magrittr_2.0.3     
[31] promises_1.3.0      ellipsis_0.3.2      htmltools_0.5.8.1  
[34] mime_0.12           xtable_1.8-4        httpuv_1.6.15      
[37] miniUI_0.1.1.1      cachem_1.1.0

The text was updated successfully, but these errors were encountered:

rcorces · 2024-10-20T22:56:44Z

Hi @penghy27! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

immanuelazn · 2024-10-21T04:06:02Z

Hi Penghyu27,

Thanks for trying to use ArchR! I am not confident that the package is with ArchR, as usethis is a dependency of devtools. Could you do installed.packages() for me?

penghy27 · 2024-10-22T01:24:33Z

Thank you for your response! Last night, I used R 4.2, and things seem to be working. However, I'm still encountering problems when installing extra packages using ArchR::installExtraPackages().
Below is a list of my currently installed packages. Could you please advise on how to resolve the installation issues?

Thank you!

> installed.packages()
                                    Package                              
abind                               "abind"                              
annotate                            "annotate"                           
AnnotationDbi                       "AnnotationDbi"                      
ArchR                               "ArchR"                              
askpass                             "askpass"                            
base                                "base"                               
base64enc                           "base64enc"                          
BH                                  "BH"                                 
Biobase                             "Biobase"                            
BiocFileCache                       "BiocFileCache"                      
BiocGenerics                        "BiocGenerics"                       
BiocIO                              "BiocIO"                             
BiocManager                         "BiocManager"                        
BiocParallel                        "BiocParallel"                       
BiocVersion                         "BiocVersion"                        
biomaRt                             "biomaRt"                            
Biostrings                          "Biostrings"                         
bit                                 "bit"                                
bit64                               "bit64"                              
bitops                              "bitops"                             
blob                                "blob"                               
boot                                "boot"                               
brew                                "brew"                               
brio                                "brio"                               
BSgenome                            "BSgenome"                           
BSgenome.Dmelanogaster.UCSC.dm6     "BSgenome.Dmelanogaster.UCSC.dm6"    
BSgenome.Hsapiens.UCSC.hg19         "BSgenome.Hsapiens.UCSC.hg19"        
bslib                               "bslib"                              
cachem                              "cachem"                             
Cairo                               "Cairo"                              
callr                               "callr"                              
caTools                             "caTools"                            
chromVAR                            "chromVAR"                           
circlize                            "circlize"                           
class                               "class"                              
cli                                 "cli"                                
clipr                               "clipr"                              
clue                                "clue"                               
cluster                             "cluster"                            
CNEr                                "CNEr"                               
codetools                           "codetools"                          
colorspace                          "colorspace"                         
commonmark                          "commonmark"                         
compiler                            "compiler"                           
ComplexHeatmap                      "ComplexHeatmap"                     
cowplot                             "cowplot"                            
cpp11                               "cpp11"                              
crayon                              "crayon"                             
credentials                         "credentials"                        
crosstalk                           "crosstalk"                          
curl                                "curl"                               
data.table                          "data.table"                         
datasets                            "datasets"                           
DBI                                 "DBI"                                
dbplyr                              "dbplyr"                             
DelayedArray                        "DelayedArray"                       
desc                                "desc"                               
devtools                            "devtools"                           
diffobj                             "diffobj"                            
digest                              "digest"                             
DirichletMultinomial                "DirichletMultinomial"               
doParallel                          "doParallel"                         
                                    LibPath                                                         
abind                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
annotate                            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
AnnotationDbi                       "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
ArchR                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
askpass                             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
base                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
base64enc                           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BH                                  "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
Biobase                             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocFileCache                       "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocGenerics                        "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocIO                              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocManager                         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocParallel                        "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BiocVersion                         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
biomaRt                             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
Biostrings                          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bit                                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bit64                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bitops                              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
blob                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
boot                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
brew                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
brio                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BSgenome                            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BSgenome.Dmelanogaster.UCSC.dm6     "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
BSgenome.Hsapiens.UCSC.hg19         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
bslib                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cachem                              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
Cairo                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
callr                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
caTools                             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
chromVAR                            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
circlize                            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
class                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cli                                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
clipr                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
clue                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cluster                             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
CNEr                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
codetools                           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
colorspace                          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
commonmark                          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
compiler                            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
ComplexHeatmap                      "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cowplot                             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
cpp11                               "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
crayon                              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
credentials                         "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
crosstalk                           "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
curl                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
data.table                          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
datasets                            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
DBI                                 "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
dbplyr                              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
DelayedArray                        "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
desc                                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
devtools                            "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
diffobj                             "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
digest                              "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
DirichletMultinomial                "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
doParallel                          "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
                                    Version     Priority     
abind                               "1.4-8"     NA           
annotate                            "1.74.0"    NA           
AnnotationDbi                       "1.58.0"    NA           
ArchR                               "1.0.2"     NA           
askpass                             "1.2.1"     NA           
base                                "4.2.3"     "base"       
base64enc                           "0.1-3"     NA           
BH                                  "1.84.0-0"  NA           
Biobase                             "2.56.0"    NA           
BiocFileCache                       "2.4.0"     NA           
BiocGenerics                        "0.42.0"    NA           
BiocIO                              "1.6.0"     NA           
BiocManager                         "1.30.25"   NA           
BiocParallel                        "1.30.4"    NA           
BiocVersion                         "3.15.2"    NA           
biomaRt                             "2.52.0"    NA           
Biostrings                          "2.64.1"    NA           
bit                                 "4.5.0"     NA           
bit64                               "4.5.2"     NA           
bitops                              "1.0-9"     NA           
blob                                "1.2.4"     NA           
boot                                "1.3-31"    "recommended"
brew                                "1.0-10"    NA           
brio                                "1.1.5"     NA           
BSgenome                            "1.64.0"    NA           
BSgenome.Dmelanogaster.UCSC.dm6     "1.4.1"     NA           
BSgenome.Hsapiens.UCSC.hg19         "1.4.3"     NA           
bslib                               "0.8.0"     NA           
cachem                              "1.1.0"     NA           
Cairo                               "1.6-2"     NA           
callr                               "3.7.6"     NA           
caTools                             "1.18.3"    NA           
chromVAR                            "1.18.0"    NA           
circlize                            "0.4.16"    NA           
class                               "7.3-22"    "recommended"
cli                                 "3.6.3"     NA           
clipr                               "0.8.0"     NA           
clue                                "0.3-65"    NA           
cluster                             "2.1.6"     "recommended"
CNEr                                "1.32.0"    NA           
codetools                           "0.2-20"    "recommended"
colorspace                          "2.1-1"     NA           
commonmark                          "1.9.2"     NA           
compiler                            "4.2.3"     "base"       
ComplexHeatmap                      "2.12.1"    NA           
cowplot                             "1.1.3"     NA           
cpp11                               "0.5.0"     NA           
crayon                              "1.5.3"     NA           
credentials                         "2.0.2"     NA           
crosstalk                           "1.2.1"     NA           
curl                                "5.2.3"     NA           
data.table                          "1.16.2"    NA           
datasets                            "4.2.3"     "base"       
DBI                                 "1.2.3"     NA           
dbplyr                              "2.5.0"     NA           
DelayedArray                        "0.22.0"    NA           
desc                                "1.4.3"     NA           
devtools                            "2.4.5"     NA           
diffobj                             "0.3.5"     NA           
digest                              "0.6.37"    NA           
DirichletMultinomial                "1.38.0"    NA           
doParallel                          "1.0.17"    NA           
                                    Depends                                                                                                                                                                                                                                
abind                               "R (>= 1.5.0)"                                                                                                                                                                                                                         
annotate                            "R (>= 2.10), AnnotationDbi (>= 1.27.5), XML"                                                                                                                                                                                          
AnnotationDbi                       "R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=\n0.29.2), Biobase (>= 1.17.0), IRanges"                                                                                                                                        
ArchR                               ""                                                                                                                                                                                                                                     
askpass                             NA                                                                                                                                                                                                                                     
base                                NA                                                                                                                                                                                                                                     
base64enc                           "R (>= 2.9.0)"                                                                                                                                                                                                                         
BH                                  NA                                                                                                                                                                                                                                     
Biobase                             "R (>= 2.10), BiocGenerics (>= 0.27.1), utils"                                                                                                                                                                                         
BiocFileCache                       "R (>= 3.4.0), dbplyr (>= 1.0.0)"                                                                                                                                                                                                      
BiocGenerics                        "R (>= 4.0.0), methods, utils, graphics, stats"                                                                                                                                                                                        
BiocIO                              "R (>= 4.0)"                                                                                                                                                                                                                           
BiocManager                         NA                                                                                                                                                                                                                                     
BiocParallel                        "methods, R (>= 3.5.0)"                                                                                                                                                                                                                
BiocVersion                         "R (>= 4.2.0)"                                                                                                                                                                                                                         
biomaRt                             "methods"                                                                                                                                                                                                                              
Biostrings                          "R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=\n0.27.12), IRanges (>= 2.30.1), XVector (>= 0.29.2),\nGenomeInfoDb"                                                                                                    
bit                                 "R (>= 3.4.0)"                                                                                                                                                                                                                         
bit64                               "R (>= 3.0.1), bit (>= 4.0.0), utils, methods, stats"                                                                                                                                                                                  
bitops                              NA                                                                                                                                                                                                                                     
blob                                NA                                                                                                                                                                                                                                     
boot                                "R (>= 3.0.0), graphics, stats"                                                                                                                                                                                                        
brew                                NA                                                                                                                                                                                                                                     
brio                                "R (>= 3.6)"                                                                                                                                                                                                                           
BSgenome                            "R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=\n0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6),\nGenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer\n(>= 1.39.7)"                              
BSgenome.Dmelanogaster.UCSC.dm6     "BSgenome (>= 1.35.10)"                                                                                                                                                                                                                
BSgenome.Hsapiens.UCSC.hg19         "BSgenome (>= 1.54.0)"                                                                                                                                                                                                                 
bslib                               "R (>= 2.10)"                                                                                                                                                                                                                          
cachem                              NA                                                                                                                                                                                                                                     
Cairo                               "R (>= 2.4.0)"                                                                                                                                                                                                                         
callr                               "R (>= 3.4)"                                                                                                                                                                                                                           
caTools                             "R (>= 3.6.0)"                                                                                                                                                                                                                         
chromVAR                            "R (>= 3.5.0)"                                                                                                                                                                                                                         
circlize                            "R (>= 4.0.0), graphics"                                                                                                                                                                                                               
class                               "R (>= 3.0.0), stats, utils"                                                                                                                                                                                                           
cli                                 "R (>= 3.4)"                                                                                                                                                                                                                           
clipr                               NA                                                                                                                                                                                                                                     
clue                                "R (>= 3.2.0)"                                                                                                                                                                                                                         
cluster                             "R (>= 3.5.0)"                                                                                                                                                                                                                         
CNEr                                "R (>= 3.5.0)"                                                                                                                                                                                                                         
codetools                           "R (>= 2.1)"                                                                                                                                                                                                                           
colorspace                          "R (>= 3.0.0), methods"                                                                                                                                                                                                                
commonmark                          NA                                                                                                                                                                                                                                     
compiler                            NA                                                                                                                                                                                                                                     
ComplexHeatmap                      "R (>= 3.5.0), methods, grid, graphics, stats, grDevices"                                                                                                                                                                              
cowplot                             "R (>= 3.5.0)"                                                                                                                                                                                                                         
cpp11                               "R (>= 3.6.0)"                                                                                                                                                                                                                         
crayon                              NA                                                                                                                                                                                                                                     
credentials                         NA                                                                                                                                                                                                                                     
crosstalk                           NA                                                                                                                                                                                                                                     
curl                                "R (>= 3.0.0)"                                                                                                                                                                                                                         
data.table                          "R (>= 3.3.0)"                                                                                                                                                                                                                         
datasets                            NA                                                                                                                                                                                                                                     
DBI                                 "methods, R (>= 3.0.0)"                                                                                                                                                                                                                
dbplyr                              "R (>= 3.6)"                                                                                                                                                                                                                           
DelayedArray                        "R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=\n0.37.0), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),\nIRanges (>= 2.17.3)"                                                                                             
desc                                "R (>= 3.4)"                                                                                                                                                                                                                           
devtools                            "R (>= 3.0.2), usethis (>= 2.1.6)"                                                                                                                                                                                                     
diffobj                             "R (>= 3.1.0)"                                                                                                                                                                                                                         
digest                              "R (>= 3.3.0)"                                                                                                                                                                                                                         
DirichletMultinomial                "S4Vectors, IRanges"                                                                                                                                                                                                                   
doParallel                          "R (>= 2.14.0), foreach (>= 1.2.0), iterators (>= 1.0.0),\nparallel, utils"                                                                                                                                                            
                                    Imports                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
abind                               "methods, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                          
annotate                            "Biobase, DBI, xtable, graphics, utils, stats, methods,\nBiocGenerics (>= 0.13.8), httr"                                                                                                                                                                                                                                                                                                                                                                                  
AnnotationDbi                       "DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST"                                                                                                                                                                                                                                                                                                                                                                                                                    
ArchR                               "ggplot2, SummarizedExperiment, data.table, Matrix, rhdf5,\nmagrittr, S4Vectors (>= 0.9.25), BiocGenerics, Rcpp (>=\n0.12.16), matrixStats, plyr, nabor, motifmatchr, chromVAR,\nuwot, ggrepel, Rsamtools, gtable, gtools, stringr, grid,\ngridExtra, Biostrings, ComplexHeatmap, GenomicRanges"                                                                                                                                                                          
askpass                             "sys (>= 2.1)"                                                                                                                                                                                                                                                                                                                                                                                                                                                            
base                                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
base64enc                           NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
BH                                  NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
Biobase                             "methods"                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
BiocFileCache                       "methods, stats, utils, dplyr, RSQLite, DBI, rappdirs,\nfilelock, curl, httr"                                                                                                                                                                                                                                                                                                                                                                                             
BiocGenerics                        "methods, utils, graphics, stats"                                                                                                                                                                                                                                                                                                                                                                                                                                         
BiocIO                              "BiocGenerics, S4Vectors, methods, tools"                                                                                                                                                                                                                                                                                                                                                                                                                                 
BiocManager                         "utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
BiocParallel                        "stats, utils, futile.logger, parallel, snow, codetools"                                                                                                                                                                                                                                                                                                                                                                                                                  
BiocVersion                         NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
biomaRt                             "utils, XML (>= 3.99-0.7), AnnotationDbi, progress, stringr,\nhttr, digest, BiocFileCache, rappdirs, xml2"                                                                                                                                                                                                                                                                                                                                                                
Biostrings                          "methods, utils, grDevices, graphics, stats, crayon"                                                                                                                                                                                                                                                                                                                                                                                                                      
bit                                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
bit64                               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
bitops                              NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
blob                                "methods, rlang, vctrs (>= 0.2.1)"                                                                                                                                                                                                                                                                                                                                                                                                                                        
boot                                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
brew                                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
brio                                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
BSgenome                            "methods, utils, stats, matrixStats, BiocGenerics, S4Vectors,\nIRanges, XVector (>= 0.29.3), GenomeInfoDb, GenomicRanges,\nBiostrings, Rsamtools, rtracklayer"                                                                                                                                                                                                                                                                                                            
BSgenome.Dmelanogaster.UCSC.dm6     "BSgenome"                                                                                                                                                                                                                                                                                                                                                                                                                                                                
BSgenome.Hsapiens.UCSC.hg19         "BSgenome"                                                                                                                                                                                                                                                                                                                                                                                                                                                                
bslib                               "base64enc, cachem, fastmap (>= 1.1.1), grDevices, htmltools\n(>= 0.5.8), jquerylib (>= 0.1.3), jsonlite, lifecycle, memoise\n(>= 2.0.1), mime, rlang, sass (>= 0.4.9)"                                                                                                                                                                                                                                                                                                   
cachem                              "rlang, fastmap (>= 1.2.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                               
Cairo                               "grDevices, graphics"                                                                                                                                                                                                                                                                                                                                                                                                                                                     
callr                               "processx (>= 3.6.1), R6, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                          
caTools                             "bitops"                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
chromVAR                            "IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor,\nBiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools,\nS4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats,\nutils, graphics, DT, Rtsne, Matrix, SummarizedExperiment,\nRColorBrewer, BSgenome"                                                                                                                                                                                                  
circlize                            "GlobalOptions (>= 0.1.2), shape, grDevices, utils, stats,\ncolorspace, methods, grid"                                                                                                                                                                                                                                                                                                                                                                                    
class                               "MASS"                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
cli                                 "utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
clipr                               "utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
clue                                "stats, cluster, graphics, methods"                                                                                                                                                                                                                                                                                                                                                                                                                                       
cluster                             "graphics, grDevices, stats, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                       
CNEr                                "Biostrings (>= 2.33.4), DBI (>= 0.7), RSQLite (>= 0.11.4),\nGenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16),\nrtracklayer (>= 1.25.5), XVector (>= 0.5.4), GenomicAlignments\n(>= 1.1.9), methods, S4Vectors (>= 0.13.13), IRanges (>=\n2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel,\nreshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3),\nannotate (>= 1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0),\nKEGGREST (>= 1.14.0)"                
codetools                           NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
colorspace                          "graphics, grDevices, stats"                                                                                                                                                                                                                                                                                                                                                                                                                                              
commonmark                          NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
compiler                            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
ComplexHeatmap                      "circlize (>= 0.4.14), GetoptLong, colorspace, clue,\nRColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,\nmatrixStats, foreach, doParallel, codetools"                                                                                                                                                                                                                                                                                                         
cowplot                             "ggplot2 (>= 3.4.0), grid, gtable, grDevices, methods, rlang,\nscales"                                                                                                                                                                                                                                                                                                                                                                                                    
cpp11                               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
crayon                              "grDevices, methods, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                               
credentials                         "openssl (>= 1.3), sys (>= 2.1), curl, jsonlite, askpass"                                                                                                                                                                                                                                                                                                                                                                                                                 
crosstalk                           "htmltools (>= 0.3.6), jsonlite, lazyeval, R6"                                                                                                                                                                                                                                                                                                                                                                                                                            
curl                                NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
data.table                          "methods"                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
datasets                            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
DBI                                 NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
dbplyr                              "blob (>= 1.2.0), cli (>= 3.6.1), DBI (>= 1.1.3), dplyr (>=\n1.1.2), glue (>= 1.6.2), lifecycle (>= 1.0.3), magrittr,\nmethods, pillar (>= 1.9.0), purrr (>= 1.0.1), R6 (>= 2.2.2),\nrlang (>= 1.1.1), tibble (>= 3.2.1), tidyr (>= 1.3.0),\ntidyselect (>= 1.2.1), utils, vctrs (>= 0.6.3), withr (>=\n2.5.0)"                                                                                                                                                           
DelayedArray                        "stats"                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
desc                                "cli, R6, utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                          
devtools                            "cli (>= 3.3.0), desc (>= 1.4.1), ellipsis (>= 0.3.2), fs (>=\n1.5.2), lifecycle (>= 1.0.1), memoise (>= 2.0.1), miniUI (>=\n0.1.1.1), pkgbuild (>= 1.3.1), pkgdown (>= 2.0.6), pkgload (>=\n1.3.0), profvis (>= 0.3.7), rcmdcheck (>= 1.4.0), remotes (>=\n2.4.2), rlang (>= 1.0.4), roxygen2 (>= 7.2.1), rversions (>=\n2.1.1), sessioninfo (>= 1.2.2), stats, testthat (>= 3.1.5),\ntools, urlchecker (>= 1.0.1), utils, withr (>= 2.5.0)"                             
diffobj                             "crayon (>= 1.3.2), tools, methods, utils, stats"                                                                                                                                                                                                                                                                                                                                                                                                                         
digest                              "utils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
DirichletMultinomial                "stats4, methods, BiocGenerics"                                                                                                                                                                                                                                                                                                                                                                                                                                           
doParallel                          NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                    LinkingTo                                                     
abind                               NA                                                            
annotate                            NA                                                            
AnnotationDbi                       NA                                                            
ArchR                               "Rcpp"                                                        
askpass                             NA                                                            
base                                NA                                                            
base64enc                           NA                                                            
BH                                  NA                                                            
Biobase                             NA                                                            
BiocFileCache                       NA                                                            
BiocGenerics                        NA                                                            
BiocIO                              NA                                                            
BiocManager                         NA                                                            
BiocParallel                        "BH"                                                          
BiocVersion                         NA                                                            
biomaRt                             NA                                                            
Biostrings                          "S4Vectors, IRanges, XVector"                                 
bit                                 NA                                                            
bit64                               NA                                                            
bitops                              NA                                                            
blob                                NA                                                            
boot                                NA                                                            
brew                                NA                                                            
brio                                NA                                                            
BSgenome                            NA                                                            
BSgenome.Dmelanogaster.UCSC.dm6     NA                                                            
BSgenome.Hsapiens.UCSC.hg19         NA                                                            
bslib                               NA                                                            
cachem                              NA                                                            
Cairo                               NA                                                            
callr                               NA                                                            
caTools                             NA                                                            
chromVAR                            "Rcpp, RcppArmadillo"                                         
circlize                            NA                                                            
class                               NA                                                            
cli                                 NA                                                            
clipr                               NA                                                            
clue                                NA                                                            
cluster                             NA                                                            
CNEr                                "S4Vectors, IRanges, XVector"                                 
codetools                           NA                                                            
colorspace                          NA                                                            
commonmark                          NA                                                            
compiler                            NA                                                            
ComplexHeatmap                      NA                                                            
cowplot                             NA                                                            
cpp11                               NA                                                            
crayon                              NA                                                            
credentials                         NA                                                            
crosstalk                           NA                                                            
curl                                NA                                                            
data.table                          NA                                                            
datasets                            NA                                                            
DBI                                 NA                                                            
dbplyr                              NA                                                            
DelayedArray                        "S4Vectors"                                                   
desc                                NA                                                            
devtools                            NA                                                            
diffobj                             NA                                                            
digest                              NA                                                            
DirichletMultinomial                NA                                                            
doParallel                          NA                                                            
                                    Suggests                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
abind                               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
annotate                            "hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,\nrae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,\norg.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit,"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
AnnotationDbi                       "hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit,\nTxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db,\nAnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
ArchR                               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
askpass                             "testthat"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
base                                "methods"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
base64enc                           NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
BH                                  NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
Biobase                             "tools, tkWidgets, ALL, RUnit, golubEsets"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
BiocFileCache                       "testthat, knitr, BiocStyle, rmarkdown, rtracklayer"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
BiocGenerics                        "Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,\nBiostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2,\nflowClust, MSnbase, annotate, RUnit"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
BiocIO                              "testthat, knitr, rmarkdown, BiocStyle"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
BiocManager                         "BiocVersion, BiocStyle, remotes, rmarkdown, testthat, withr,\ncurl, knitr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
BiocParallel                        "BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,\nRmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,\nTxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,\nRsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,\nknitr, batchtools, data.table"                                                                                                                                                                                                                                                                                                                                                                                         
BiocVersion                         NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
biomaRt                             "BiocStyle, knitr, rmarkdown, testthat, mockery"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
Biostrings                          "BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=\n1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),\nBSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,\nhgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy\n(>= 1.41.3), affydata (>= 1.11.5), RUnit"                                                                                                                                                                                                                                                                                                                                                                       
bit                                 "testthat (>= 0.11.0), roxygen2, knitr, markdown, rmarkdown,\nmicrobenchmark, bit64 (>= 4.0.0), ff (>= 4.0.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
bit64                               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
bitops                              NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
blob                                "covr, crayon, pillar (>= 1.2.1), testthat"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
boot                                "MASS, survival"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
brew                                "testthat (>= 3.0.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
brio                                "covr, testthat (>= 3.0.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
BSgenome                            "BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,\nBSgenome.Hsapiens.UCSC.hg38,\nBSgenome.Hsapiens.UCSC.hg38.masked,\nBSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,\nBSgenome.Scerevisiae.UCSC.sacCer1,\nBSgenome.Hsapiens.NCBI.GRCh38,\nTxDb.Hsapiens.UCSC.hg38.knownGene,\nTxDb.Mmusculus.UCSC.mm10.knownGene,\nSNPlocs.Hsapiens.dbSNP144.GRCh38,\nXtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit"                                                                                                                                                                                                                            
BSgenome.Dmelanogaster.UCSC.dm6     "GenomicFeatures"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
BSgenome.Hsapiens.UCSC.hg19         ""                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
bslib                               "bsicons, curl, fontawesome, future, ggplot2, knitr, magrittr,\nrappdirs, rmarkdown (>= 2.7), shiny (> 1.8.1), testthat,\nthematic, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
cachem                              "testthat"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Cairo                               "png"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
callr                               "asciicast (>= 2.3.1), cli (>= 1.1.0), mockery, ps, rprojroot,\nspelling, testthat (>= 3.2.0), withr (>= 2.3.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
caTools                             "MASS, rpart"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
chromVAR                            "JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat,\nknitr, rmarkdown, pheatmap, motifmatchr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
circlize                            "knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0),\ngridBase, png, markdown, bezier, covr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
class                               NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
cli                                 "callr, covr, crayon, digest, glue (>= 1.6.0), grDevices,\nhtmltools, htmlwidgets, knitr, methods, mockery, processx, ps\n(>= 1.3.4.9000), rlang (>= 1.0.2.9003), rmarkdown, rprojroot,\nrstudioapi, testthat, tibble, whoami, withr"                                                                                                                                                                                                                                                                                                                                                                                                                       
clipr                               "covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>=\n2.0.0)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
clue                                "e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
cluster                             "MASS, Matrix"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
CNEr                                "Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat,\nBSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,\nTxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19,\nBSgenome.Ggallus.UCSC.galGal3"                                                                                                                                                                                                                                                                                                                                                                                                                                      
codetools                           NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
colorspace                          "datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd,\ntcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg,\nknitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis,\nwesanderson"                                                                                                                                                                                                                                                                                                                                                                                                                                                     
commonmark                          "curl, testthat, xml2"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
compiler                            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
ComplexHeatmap                      "testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,\nfastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,\ngrImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),\ngridGraphics, gplots, rmarkdown, Cairo"                                                                                                                                                                                                                                                                                                                                                                                                                      
cowplot                             "Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr,\nlattice, magick, maps, PASWR, patchwork, rmarkdown, ragg,\ntestthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram"                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
cpp11                               "bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,\nknitr, lobstr, mockery, progress, rmarkdown, scales, Rcpp,\ntestthat (>= 3.2.0), tibble, utils, vctrs, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
crayon                              "mockery, rstudioapi, testthat, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
credentials                         "testthat, knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
crosstalk                           "shiny, ggplot2, testthat (>= 2.1.0), sass, bslib"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
curl                                "spelling, testthat (>= 1.0.0), knitr, jsonlite, later,\nrmarkdown, httpuv (>= 1.4.4), webutils"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
data.table                          "bit64 (>= 4.0.0), bit (>= 4.0.4), R.utils, xts, zoo (>=\n1.8-1), yaml, knitr, markdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
datasets                            NA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
DBI                                 "arrow, blob, covr, DBItest, dbplyr, downlit, dplyr, glue,\nhms, knitr, magrittr, nanoarrow (>= 0.3.0.1), RMariaDB,\nrmarkdown, rprojroot, RSQLite (>= 1.1-2), testthat (>= 3.0.0),\nvctrs, xml2"                                                                                                                                                                                                                                                                                                                                                                                                                                                           
dbplyr                              "bit64, covr, knitr, Lahman, nycflights13, odbc (>= 1.4.2),\nRMariaDB (>= 1.2.2), rmarkdown, RPostgres (>= 1.4.5),\nRPostgreSQL, RSQLite (>= 2.3.1), testthat (>= 3.1.10)"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
DelayedArray                        "BiocParallel, HDF5Array (>= 1.17.12), genefilter,\nSummarizedExperiment, airway, lobstr, DelayedMatrixStats,\nknitr, rmarkdown, BiocStyle, RUnit"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
desc                                "callr, covr, gh, spelling, testthat, whoami, withr"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
devtools                            "BiocManager (>= 1.30.18), callr (>= 3.7.1), covr (>= 3.5.1),\ncurl (>= 4.3.2), digest (>= 0.6.29), DT (>= 0.23), foghorn (>=\n1.4.2), gh (>= 1.3.0), gmailr (>= 1.0.1), httr (>= 1.4.3),\nknitr (>= 1.39), lintr (>= 3.0.0), MASS, mockery (>= 0.4.3),\npingr (>= 2.0.1), rhub (>= 1.1.1), rmarkdown (>= 2.14),\nrstudioapi (>= 0.13), spelling (>= 2.2)"                                                                                                                                                                                                                                                                                                  
diffobj                             "knitr, rmarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
digest                              "tinytest, simplermarkdown"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
DirichletMultinomial                "lattice, parallel, MASS, RColorBrewer, xtable"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
doParallel                          "caret, mlbench, rpart, RUnit"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                    Enhances                                                                          
abind                               NA                                                                                
annotate                            NA                                                                                
AnnotationDbi                       NA                                                                                
ArchR                               NA                                                                                
askpass                             NA                                                                                
base                                NA                                                                                
base64enc                           "png"                                                                             
BH                                  NA                                                                                
Biobase                             NA                                                                                
BiocFileCache                       NA                                                                                
BiocGenerics                        NA                                                                                
BiocIO                              NA                                                                                
BiocManager                         NA                                                                                
BiocParallel                        NA                                                                                
BiocVersion                         NA                                                                                
biomaRt                             NA                                                                                
Biostrings                          "Rmpi"                                                                            
bit                                 NA                                                                                
bit64                               NA                                                                                
bitops                              NA                                                                                
blob                                NA                                                                                
boot                                NA                                                                                
brew                                NA                                                                                
brio                                NA                                                                                
BSgenome                            NA                                                                                
BSgenome.Dmelanogaster.UCSC.dm6     NA                                                                                
BSgenome.Hsapiens.UCSC.hg19         NA                                                                                
bslib                               NA                                                                                
cachem                              NA                                                                                
Cairo                               "FastRWeb"                                                                        
callr                               NA                                                                                
caTools                             NA                                                                                
chromVAR                            NA                                                                                
circlize                            NA                                                                                
class                               NA                                                                                
cli                                 NA                                                                                
clipr                               NA                                                                                
clue                                "RWeka, ape, cba, cclust, flexclust, flexmix, kernlab, mclust,\nmovMF, modeltools"
cluster                             "mvoutlier, fpc, ellipse, sfsmisc"                                                
CNEr                                NA                                                                                
codetools                           NA                                                                                
colorspace                          NA                                                                                
commonmark                          NA                                                                                
compiler                            NA                                                                                
ComplexHeatmap                      NA                                                                                
cowplot                             NA                                                                                
cpp11                               NA                                                                                
crayon                              NA                                                                                
credentials                         NA                                                                                
crosstalk                           NA                                                                                
curl                                NA                                                                                
data.table                          NA                                                                                
datasets                            NA                                                                                
DBI                                 NA                                                                                
dbplyr                              NA                                                                                
DelayedArray                        NA                                                                                
desc                                NA                                                                                
devtools                            NA                                                                                
diffobj                             NA                                                                                
digest                              NA                                                                                
DirichletMultinomial                NA                                                                                
doParallel                          "compiler"                                                                        
                                    License                                  License_is_FOSS
abind                               "MIT + file LICENSE"                     NA             
annotate                            "Artistic-2.0"                           NA             
AnnotationDbi                       "Artistic-2.0"                           NA             
ArchR                               "GPL (>= 2)"                             NA             
askpass                             "MIT + file LICENSE"                     NA             
base                                "Part of R 4.2.3"                        NA             
base64enc                           "GPL-2 | GPL-3"                          NA             
BH                                  "BSL-1.0"                                NA             
Biobase                             "Artistic-2.0"                           NA             
BiocFileCache                       "Artistic-2.0"                           NA             
BiocGenerics                        "Artistic-2.0"                           NA             
BiocIO                              "Artistic-2.0"                           NA             
BiocManager                         "Artistic-2.0"                           NA             
BiocParallel                        "GPL-2 | GPL-3"                          NA             
BiocVersion                         "Artistic-2.0"                           NA             
biomaRt                             "Artistic-2.0"                           NA             
Biostrings                          "Artistic-2.0"                           NA             
bit                                 "GPL-2 | GPL-3"                          NA             
bit64                               "GPL-2 | GPL-3"                          NA             
bitops                              "GPL (>= 2)"                             NA             
blob                                "MIT + file LICENSE"                     NA             
boot                                "Unlimited"                              NA             
brew                                "GPL (>= 2)"                             NA             
brio                                "MIT + file LICENSE"                     NA             
BSgenome                            "Artistic-2.0"                           NA             
BSgenome.Dmelanogaster.UCSC.dm6     "Artistic-2.0"                           NA             
BSgenome.Hsapiens.UCSC.hg19         "Artistic-2.0"                           NA             
bslib                               "MIT + file LICENSE"                     NA             
cachem                              "MIT + file LICENSE"                     NA             
Cairo                               "GPL-2 | GPL-3"                          NA             
callr                               "MIT + file LICENSE"                     NA             
caTools                             "GPL-3"                                  NA             
chromVAR                            "MIT + file LICENSE"                     NA             
circlize                            "MIT + file LICENSE"                     NA             
class                               "GPL-2 | GPL-3"                          NA             
cli                                 "MIT + file LICENSE"                     NA             
clipr                               "GPL-3"                                  NA             
clue                                "GPL-2"                                  NA             
cluster                             "GPL (>= 2)"                             NA             
CNEr                                "GPL-2 | file LICENSE"                   NA             
codetools                           "GPL"                                    NA             
colorspace                          "BSD_3_clause + file LICENSE"            NA             
commonmark                          "BSD_2_clause + file LICENSE"            NA             
compiler                            "Part of R 4.2.3"                        NA             
ComplexHeatmap                      "MIT + file LICENSE"                     NA             
cowplot                             "GPL-2"                                  NA             
cpp11                               "MIT + file LICENSE"                     NA             
crayon                              "MIT + file LICENSE"                     NA             
credentials                         "MIT + file LICENSE"                     NA             
crosstalk                           "MIT + file LICENSE"                     NA             
curl                                "MIT + file LICENSE"                     NA             
data.table                          "MPL-2.0 | file LICENSE"                 NA             
datasets                            "Part of R 4.2.3"                        NA             
DBI                                 "LGPL (>= 2.1)"                          NA             
dbplyr                              "MIT + file LICENSE"                     NA             
DelayedArray                        "Artistic-2.0"                           NA             
desc                                "MIT + file LICENSE"                     NA             
devtools                            "MIT + file LICENSE"                     NA             
diffobj                             "GPL-2 | GPL-3"                          NA             
digest                              "GPL (>= 2)"                             NA             
DirichletMultinomial                "LGPL-3"                                 NA             
doParallel                          "GPL-2"                                  NA             
                                    License_restricts_use OS_type MD5sum NeedsCompilation Built  
abind                               NA                    NA      NA     "no"             "4.2.3"
annotate                            NA                    NA      NA     "no"             "4.2.0"
AnnotationDbi                       NA                    NA      NA     "no"             "4.2.0"
ArchR                               NA                    NA      NA     "yes"            "4.2.3"
askpass                             NA                    NA      NA     "yes"            "4.2.3"
base                                NA                    NA      NA     NA               "4.2.3"
base64enc                           NA                    NA      NA     "yes"            "4.2.0"
BH                                  NA                    NA      NA     "no"             "4.2.3"
Biobase                             NA                    NA      NA     "yes"            "4.2.0"
BiocFileCache                       NA                    NA      NA     "no"             "4.2.0"
BiocGenerics                        NA                    NA      NA     "no"             "4.2.0"
BiocIO                              NA                    NA      NA     "no"             "4.2.0"
BiocManager                         NA                    NA      NA     "no"             "4.2.3"
BiocParallel                        NA                    NA      NA     "yes"            "4.2.1"
BiocVersion                         NA                    NA      NA     "no"             "4.2.0"
biomaRt                             NA                    NA      NA     "no"             "4.2.0"
Biostrings                          NA                    NA      NA     "yes"            "4.2.1"
bit                                 NA                    NA      NA     "yes"            "4.2.3"
bit64                               NA                    NA      NA     "yes"            "4.2.3"
bitops                              NA                    NA      NA     "yes"            "4.2.3"
blob                                NA                    NA      NA     "no"             "4.2.0"
boot                                NA                    NA      NA     "no"             "4.2.3"
brew                                NA                    NA      NA     "no"             "4.2.0"
brio                                NA                    NA      NA     "yes"            "4.2.3"
BSgenome                            NA                    NA      NA     "no"             "4.2.0"
BSgenome.Dmelanogaster.UCSC.dm6     NA                    NA      NA     NA               "4.2.3"
BSgenome.Hsapiens.UCSC.hg19         NA                    NA      NA     "no"             "4.2.3"
bslib                               NA                    NA      NA     "no"             "4.2.3"
cachem                              NA                    NA      NA     "yes"            "4.2.3"
Cairo                               NA                    NA      NA     "yes"            "4.2.0"
callr                               NA                    NA      NA     "no"             "4.2.3"
caTools                             NA                    NA      NA     "yes"            "4.2.3"
chromVAR                            NA                    NA      NA     "yes"            "4.2.0"
circlize                            NA                    NA      NA     "no"             "4.2.3"
class                               NA                    NA      NA     "yes"            "4.2.0"
cli                                 NA                    NA      NA     "yes"            "4.2.3"
clipr                               NA                    NA      NA     "no"             "4.2.0"
clue                                NA                    NA      NA     "yes"            "4.2.0"
cluster                             NA                    NA      NA     "yes"            "4.2.0"
CNEr                                "yes"                 NA      NA     "yes"            "4.2.0"
codetools                           NA                    NA      NA     "no"             "4.2.3"
colorspace                          NA                    NA      NA     "yes"            "4.2.3"
commonmark                          NA                    NA      NA     "yes"            "4.2.3"
compiler                            NA                    NA      NA     NA               "4.2.3"
ComplexHeatmap                      NA                    NA      NA     "no"             "4.2.1"
cowplot                             NA                    NA      NA     "no"             "4.2.3"
cpp11                               NA                    NA      NA     "no"             "4.2.3"
crayon                              NA                    NA      NA     "no"             "4.2.3"
credentials                         NA                    NA      NA     "no"             "4.2.3"
crosstalk                           NA                    NA      NA     "no"             "4.2.0"
curl                                NA                    NA      NA     "yes"            "4.2.3"
data.table                          NA                    NA      NA     "yes"            "4.2.3"
datasets                            NA                    NA      NA     NA               "4.2.3"
DBI                                 NA                    NA      NA     "no"             "4.2.3"
dbplyr                              NA                    NA      NA     "no"             "4.2.3"
DelayedArray                        NA                    NA      NA     "yes"            "4.2.0"
desc                                NA                    NA      NA     "no"             "4.2.0"
devtools                            NA                    NA      NA     "no"             "4.2.0"
diffobj                             NA                    NA      NA     "yes"            "4.2.0"
digest                              NA                    NA      NA     "yes"            "4.2.3"
DirichletMultinomial                NA                    NA      NA     "yes"            "4.2.0"
doParallel                          NA                    NA      NA     "no"             "4.2.0"
 [ reached getOption("max.print") -- omitted 224 rows ]

immanuelazn · 2024-10-22T01:51:28Z

Hi Penghy27, Are you getting the same issue with installExtraPackages() with usethis? Overall the function just tries to install Seurat, Cairo, harmony, preswto, shiny, rhandsontable and shinythemes. I see you have Cairo, but are you getting an error with installation of the other packages?

Best,

Immanuel

penghy27 · 2024-10-22T02:06:25Z

Hi Immanuel, Thanks for your prompt response. Yes, I have Cairo installed, but I encountered errors on Seurat, igraph, dotCall64, spam, spatstat.geom, and spatstat.random. I used install.packages() to install these packages, but the errors persist. The error messages indicate issues with multiple dependencies during the installation of the Seurat package.

For example, when I try to install Seurat, I encounter errors like the one above. I also attempted to install other packages, such as igraph and spam, but the issues persist.

Thank you for your assistance.

Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-igraph/00new/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-igraph/00new/igraph/libs/igraph.so, 0x0006): symbol not found in flat namespace '_igraphdnaupd_'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/igraph’
Warning in install.packages :
  installation of package ‘igraph’ had non-zero exit status
ERROR: dependency ‘dotCall64’ is not available for package ‘spam’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spam’
Warning in install.packages :
  installation of package ‘spam’ had non-zero exit status
ERROR: dependency ‘deldir’ is not available for package ‘spatstat.geom’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spatstat.geom’
Warning in install.packages :
  installation of package ‘spatstat.geom’ had non-zero exit status
ERROR: dependency ‘spatstat.geom’ is not available for package ‘spatstat.random’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spatstat.random’
Warning in install.packages :
  installation of package ‘spatstat.random’ had non-zero exit status
ERROR: dependency ‘spam’ is not available for package ‘SeuratObject’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/SeuratObject’
Warning in install.packages :
  installation of package ‘SeuratObject’ had non-zero exit status
ERROR: dependencies ‘spatstat.geom’, ‘spatstat.random’ are not available for package ‘spatstat.explore’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/spatstat.explore’
Warning in install.packages :
  installation of package ‘spatstat.explore’ had non-zero exit status
ERROR: dependencies ‘SeuratObject’, ‘igraph’, ‘spatstat.explore’, ‘spatstat.geom’ are not available for package ‘Seurat’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Seurat’
Warning in install.packages :
  installation of package ‘Seurat’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/l8/b2285nqj68x2y4sdjnfwd4v80000gn/T/RtmpmwvVr1/downloaded_packages’

immanuelazn · 2024-10-22T02:16:28Z

Hi penghy27 this is something I'm not 100% familiar with and it seems like a system issue with your R environment and your compiler. When I read through some other literature, I see that you could alleviate this by by going into ~/.R/Makevars and setting your compiler to clang.

CC = clang
CXX = clang++

Could you try doing this, restarting your R environment, and try reinstalling a few of the packages?

penghy27 · 2024-10-22T13:46:55Z

Hi Immanuel, thank you for your suggestions. Unfortunately, reinstalling the packages still failed after setting the compiler to clang, even after restarting the R environment and macOS. It's strange that I can't load the ArchR library after the restart. Maybe I need to check the dependencies or any conflicts in the environment.
Could you share the information what version of R, Bioconductor, and operation system you use?

penghy27 added the bug Something isn't working label Oct 20, 2024

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