Annotation hub and clusterProfiler errors
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0
Entering edit mode
BS • 0
@33343537
Last seen 13 months ago
Norway

How can I get AnnotationHub() run? Also, clusterProfiler is not working because I am unable to install HPO.db

> ah <- AnnotationHub()

**Error in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`


   > library(clusterProfiler)

**Error: Error: package or namespace load failed for 'clusterProfiler' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'HPO.db'**

  >  BiocManager::install(version='devel')
 >   BiocManager::install("HPO.db")

Error: Bioconductor version '3.19' requires R version '4.4'; use `version = '3.18'` with R version
  4.3; see https://bioconductor.org/install
Error: package or namespace load failed for 'clusterProfiler' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'HPO.db'




> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/Oslo
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] dplyr_1.1.3             AnnotationHub_3.10.0    BiocFileCache_2.10.0   
 [4] dbplyr_2.4.0            ensembldb_2.26.0        AnnotationFilter_1.26.0
 [7] GenomicFeatures_1.54.0  AnnotationDbi_1.64.0    Biobase_2.62.0         
[10] GenomicRanges_1.54.0    GenomeInfoDb_1.38.0     IRanges_2.36.0         
[13] S4Vectors_0.40.0        BiocGenerics_0.48.0    

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0              blob_1.2.4                    filelock_1.0.2               
 [4] Biostrings_2.70.0             bitops_1.0-7                  lazyeval_0.2.2               
 [7] fastmap_1.1.1                 RCurl_1.98-1.12               GenomicAlignments_1.38.0     
[10] promises_1.2.1                XML_3.99-0.14                 digest_0.6.33                
[13] mime_0.12                     lifecycle_1.0.3               ProtGenerics_1.34.0          
[16] ellipsis_0.3.2                KEGGREST_1.42.0               interactiveDisplayBase_1.40.0
[19] RSQLite_2.3.1                 magrittr_2.0.3                compiler_4.3.1               
[22] rlang_1.1.1                   progress_1.2.2                tools_4.3.1                  
[25] utf8_1.2.4                    yaml_2.3.7                    rtracklayer_1.62.0           
[28] prettyunits_1.2.0             S4Arrays_1.2.0                bit_4.0.5                    
[31] curl_5.1.0                    DelayedArray_0.28.0           xml2_1.3.5                   
[34] abind_1.4-5                   BiocParallel_1.36.0           purrr_1.0.2                  
[37] grid_4.3.1                    fansi_1.0.5                   xtable_1.8-4                 
[40] biomaRt_2.58.0                SummarizedExperiment_1.32.0   cli_3.6.1                    
[43] crayon_1.5.2                  generics_0.1.3                remotes_2.4.2.1              
[46] rstudioapi_0.15.0             httr_1.4.7                    rjson_0.2.21                 
[49] DBI_1.1.3                     cachem_1.0.8                  stringr_1.5.0                
[52] zlibbioc_1.48.0               parallel_4.3.1                BiocManager_1.30.22          
[55] XVector_0.42.0                restfulr_0.0.15               matrixStats_1.0.0            
[58] vctrs_0.6.4                   Matrix_1.5-4.1                hms_1.1.3                    
[61] bit64_4.0.5                   glue_1.6.2                    codetools_0.2-19             
[64] stringi_1.7.12                BiocVersion_3.18.0            later_1.3.1                  
[67] BiocIO_1.12.0                 tibble_3.2.1                  pillar_1.9.0                 
[70] rappdirs_0.3.3                htmltools_0.5.6.1             GenomeInfoDbData_1.2.11      
[73] R6_2.5.1                      lattice_0.21-8                shiny_1.7.5.1                
[76] png_0.1-8                     Rsamtools_2.18.0              openxlsx_4.2.5.2             
[79] memoise_2.0.1                 httpuv_1.6.12                 Rcpp_1.0.11                  
[82] zip_2.3.0                     SparseArray_1.2.0             MatrixGenerics_1.14.0        
[85] pkgconfig_2.0.3
clusterProfiler Annotationhub • 1.8k views
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@james-w-macdonald-5106
Last seen 11 hours ago
United States

See this.

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1
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Also, you probably want to use the release version, in which case you don't want to do this

BiocManager::install(version = "devel")

But if you do want to use devel, then you need to install R-devel as well, as we are in the period between Oct-Apr when you need R-devel to run Bioc-devel.

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Thank you very much for the suggestion. I have BiocFileCache version 2.10.0 with Date/Publication: 2023-10-24. Do you have any other suggestions? I reinstalled the package. However, the same error appears. Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect()

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Did you check the thread James linked to?

If you did, you would have seen that the bug has been fixed in both release and development versions of BiocFileCache. These are versions 2.10.1 (Release_3_18) and 2.11.1 (devel/3.19). Based on your info it is clear that you have still version 2.10.0 of BioFileCache installed, so NOT the version that has been fixed....! It usually takes 24h (max 48h) before an updated package comes available for download on the Bioconductor site.

You can already install the fixed (development) version directly from GitHub: BiocManager::install("Bioconductor/BiocFileCache")

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