standardChromosomes() function not found but its guide yes.

Question

[francesca3]

Hi, I'm having troubles working in R (loaded via conda env). I installed all the packages required via conda but when I tried to use the function standardChromosomes() from the package GenomeInfodb I'm just able to recall the guide with ?standardChromosomes() but not using the function itself (it says "function not found"). How it is possible? Thanks Francesca

R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /hpcnfs/home/ieo5212/.conda/envs/R/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] Signac_1.7.0

loaded via a namespace (and not attached):
 [1] SeuratObject_4.0.4     Rcpp_1.0.8             lattice_0.20-45       
 [4] tidyr_1.1.4            listenv_0.8.0          Rsamtools_2.10.0      
 [7] Biostrings_2.62.0      assertthat_0.2.1       digest_0.6.29         
[10] utf8_1.2.2             parallelly_1.30.0      IRdisplay_1.1         
[13] R6_2.5.1               GenomeInfoDb_1.30.0    repr_1.1.4            
[16] stats4_4.1.3           evaluate_0.14          ggplot2_3.3.5         
[19] pillar_1.6.4           zlibbioc_1.40.0        rlang_1.0.2           
[22] uuid_1.0-3             irlba_2.3.5            data.table_1.14.2     
[25] S4Vectors_0.32.3       Matrix_1.4-0           BiocParallel_1.28.3   
[28] RCurl_1.98-1.6         munsell_0.5.0          compiler_4.1.3        
[31] pkgconfig_2.0.3        BiocGenerics_0.40.0    base64enc_0.1-3       
[34] globals_0.14.0         htmltools_0.5.2        tidyselect_1.1.1      
[37] tibble_3.1.6           GenomeInfoDbData_1.2.7 IRanges_2.28.0        
[40] codetools_0.2-18       RcppRoll_0.3.0         fansi_1.0.2           
[43] future_1.23.0          crayon_1.4.2           dplyr_1.0.7           
[46] bitops_1.0-7           grid_4.1.3             jsonlite_1.8.0        
[49] gtable_0.3.0           lifecycle_1.0.1        DBI_1.1.2             
[52] magrittr_2.0.1         scales_1.1.1           stringi_1.7.6         
[55] pbapply_1.5-0          future.apply_1.8.1     cli_3.1.1             
[58] XVector_0.34.0         ellipsis_0.3.2         generics_0.1.1        
[61] vctrs_0.3.8            fastmatch_1.1-3        IRkernel_1.3          
[64] tools_4.1.3            glue_1.6.1             purrr_0.3.4           
[67] parallel_4.1.3         fastmap_1.1.0          colorspace_2.0-2      
[70] GenomicRanges_1.46.1   pbdZMQ_0.3-6           patchwork_1.1.1     

[cpad0112]

> packageVersion("GenomeInfoDb")
[1] ‘1.32.2’

> grep ("standardChromosomes", ls("package:GenomeInfoDb"), value = T)
[1] "standardChromosomes"

> ls("package:GenomeInfoDb")
 [1] "as.data.frame"              "as.data.frame.Seqinfo"      "bsgenomeName"              
 [4] "checkCompatibleSeqinfo"     "commonName"                 "DEFAULT_CIRC_SEQS"         
 [7] "dropSeqlevels"              "extractSeqlevels"           "extractSeqlevelsByGroup"   
[10] "genome"                     "genome<-"                   "genomeBuilds"              
[13] "GenomeDescription"          "genomeStyles"               "getChromInfoFromEnsembl"   
[16] "getChromInfoFromNCBI"       "getChromInfoFromUCSC"       "intersect"                 
[19] "isCircular"                 "isCircular<-"               "keepSeqlevels"             
[22] "keepStandardChromosomes"    "listOrganisms"              "loadTaxonomyDb"            
[25] "mapGenomeBuilds"            "mapSeqlevels"               "merge"                     
[28] "orderSeqlevels"             "organism"                   "provider"                  
[31] "providerVersion"            "rankSeqlevels"              "registered_NCBI_assemblies"
[34] "registered_UCSC_genomes"    "releaseDate"                "releaseName"               
[37] "renameSeqlevels"            "restoreSeqlevels"           "seqinfo"                   
[40] "Seqinfo"                    "seqinfo<-"                  "seqlengths"                
[43] "seqlengths<-"               "seqlevels"                  "seqlevels<-"               
[46] "seqlevels0"                 "seqlevelsInGroup"           "seqlevelsInUse"            
[49] "seqlevelsStyle"             "seqlevelsStyle<-"           "seqnames"                  
[52] "seqnames<-"                 "show"                       "sortSeqlevels"             
[55] "species"                    "standardChromosomes"        "summary"                   
[58] "summary.Seqinfo"           


> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4 
.....

[francesca3]

It is very strange. I'm able to run

packageVersion("GenomeInfoDb")

But not

ls("package:GenomeInfoDb")

I'm able to do it for other packages, but in this case it says package not found

[cpad0112]

Try reinstalling the package.

[francesca3]

In the end I created a new env conda and I installed everything again. Very boring solution but the only one that solved every problem