My clusterProfiler was working well (I don't remember which version I had). Then I tried to conduct a customized enrichment analysis in tomato following the instructions given here https://www.biostars.org/p/9544007/.

Cluster profiler could not find any match for gene IDs and reading a lot in the web, I followed the recommendation of updating R and clusterProfiler. I know have R 4.3.1 in my MacBookPro silicon M1 and clusterProfiler 4.9.2.

Now clusterProfiler is not even able to load, this is one happens:

library(clusterProfiler)

Error: package or namespace load failed for clusterProfiler:

object HPOGENE is not exported by namespace HPO.db

I have tried everything and nothing fixed the problem so far. Any help would be highly appreciated. THANKS!

sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Edmonton
tzcode source: internal

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

other attached packages:
 [1] pheatmap_1.0.12             gplots_3.1.3               
 [3] ggplot2_3.4.4               RColorBrewer_1.1-3         
 [5] DESeq2_1.42.0               SummarizedExperiment_1.32.0
 [7] Biobase_2.62.0              MatrixGenerics_1.14.0      
 [9] matrixStats_1.0.0           GenomicRanges_1.54.0       
[11] 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] KEGGREST_1.42.0         GOSemSim_2.29.0         gtable_0.3.4           
 [4] HPO.db_1.2              caTools_1.18.2          lattice_0.22-5         
 [7] vctrs_0.6.4             tools_4.3.1             bitops_1.0-7           
[10] generics_0.1.3          parallel_4.3.1          tibble_3.2.1           
[13] fansi_1.0.5             AnnotationDbi_1.64.0    RSQLite_2.3.1          
[16] blob_1.2.4              pkgconfig_2.0.3         Matrix_1.6-1.1         
[19] KernSmooth_2.23-22      lifecycle_1.0.3         GenomeInfoDbData_1.2.11
[22] HDO.db_0.99.1           compiler_4.3.1          Biostrings_2.69.2      
[25] munsell_0.5.0           codetools_0.2-19        RCurl_1.98-1.12        
[28] GO.db_3.18.0            pillar_1.9.0            crayon_1.5.2           
[31] BiocParallel_1.36.0     DelayedArray_0.28.0     cachem_1.0.8           
[34] abind_1.4-5             gtools_3.9.4            tidyselect_1.2.0       
[37] locfit_1.5-9.8          dplyr_1.1.3             fastmap_1.1.1          
[40] grid_4.3.1              colorspace_2.1-0        cli_3.6.1              
[43] SparseArray_1.2.0       magrittr_2.0.3          S4Arrays_1.2.0         
[46] utf8_1.2.4              withr_2.5.1             scales_1.2.1           
[49] bit64_4.0.5             httr_1.4.7              XVector_0.42.0         
[52] bit_4.0.5               png_0.1-8               memoise_2.0.1          
[55] rlang_1.1.1             Rcpp_1.0.11             glue_1.6.2             
[58] DBI_1.1.3               rstudioapi_0.15.0       R6_2.5.1               
[61] zlibbioc_1.48.0

The correct version of HPO.db is 0.99.2. You have version 1.2, which appears to be a completely different package from CRAN.

Hello guys, the problem is solved thanks to the tips provided by James McDonald. Here the solution, in case somebody else faces the same problem:

1. I installed BiocManager::install("Bioconductor/BiocFileCache") as described in BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR.

2. I installed HPO.db with remotes::install_github("YuLab-SMU/HPO.db")

3. I reinstalled clusterProfiler with Bioconductor.

All work good now. Thanks to all that responded to my request.

You should install the Bioconductor version of HPO.db: https://bioconductor.org/packages/release/data/annotation/html/HPO.db.html

You probably need to remove the existing version first.

> library(BiocManager)
Bioconductor version 3.18
  (BiocManager 1.30.22), R 4.3.1
  (2023-06-16 ucrt)
> remove.packages("HPO.db")
Removing package from 'C:/Users/jmacdon/AppData/Local/R/win-library/4.3'
(as 'lib' is unspecified)
> install("HPO.db")
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
Bioconductor version 3.18
  (BiocManager 1.30.22), R 4.3.1
  (2023-06-16 ucrt)
Installing package(s) 'HPO.db'
installing the source package 'HPO.db'

trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HPO.db_0.99.2.tar.gz'
Content type 'application/x-gzip' length 24377 bytes (23 KB)
downloaded 23 KB

* installing *source* package 'HPO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HPO.db)