I am using the following code to install clusterProfiler:

source("https://bioconductor.org/biocLite.R")

BiocInstaller::biocLite("clusterProfiler")

I get the following error:

Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called ‘bit’

Error : package ‘AnnotationDbi’ could not be loaded

ERROR: lazy loading failed for package ‘GO.db’

• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/GO.db’

The downloaded source packages are in

‘/private/var/folders/jm/lw5pqpvs0_j025smc3qkpl5c0000gn/T/RtmpnPsdF8/downloaded_packages’

Warning message:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘GO.db’ had non-zero exit status

I'm really not sure what to do here. When I search online, everyone pretty much says to do exactly what I did, and that it should install the required packages. I am new to R, and this is beyond me. Thanks for any help you can provide!

It looks like you have AnnotationDbi installed, but are missing dependencies. Or actually, dependencies of dependencies, as bit isn't a direct dependency of AnnotationDbi. You probably need to re-install AnnotationDbi to get all the dependencies.

Hi,

I have a similar issue, though I am not sure what is causing it. I tried to install clusterProfiler on a jupyter notebook that runs R v4.0.5 and Bioconductor v3.12. Any help would be greatly appreciated!

R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /home/theo/miniconda3/envs/sc_analysis/lib/libopenblasp-r0.3.12.so

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

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

other attached packages:
 [1] RColorBrewer_1.1-2          pheatmap_1.0.12            
 [3] reshape2_1.4.4              dplyr_1.0.7                
 [5] MAST_1.16.0                 SingleCellExperiment_1.12.0
 [7] SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [9] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
[11] IRanges_2.24.1              S4Vectors_0.28.1           
[13] BiocGenerics_0.36.1         MatrixGenerics_1.2.1       
[15] matrixStats_0.61.0          ggthemes_4.2.4             
[17] ggsci_2.9                   harmony_0.1.0              
[19] Rcpp_1.0.7                  SeuratObject_4.0.4         
[21] Seurat_4.0.5                foreach_1.5.1              
[23] useful_1.2.6                ggplot2_3.3.5              

loaded via a namespace (and not attached):
  [1] Rtsne_0.15             colorspace_2.0-2       deldir_1.0-6          
  [4] ellipsis_0.3.2         ggridges_0.5.3         IRdisplay_1.0         
  [7] XVector_0.30.0         base64enc_0.1-3        spatstat.data_2.1-0   
 [10] leiden_0.3.9           listenv_0.8.0          ggrepel_0.9.1         
 [13] fansi_0.5.0            codetools_0.2-18       splines_4.0.5         
 [16] polyclip_1.10-0        IRkernel_1.2           jsonlite_1.7.2        
 [19] ica_1.0-2              cluster_2.1.2          png_0.1-7             
 [22] uwot_0.1.10            shiny_1.7.1            sctransform_0.3.2     
 [25] spatstat.sparse_2.0-0  BiocManager_1.30.16    compiler_4.0.5        
 [28] httr_1.4.2             Matrix_1.3-4           fastmap_1.1.0         
 [31] lazyeval_0.2.2         later_1.3.0            htmltools_0.5.2       
 [34] tools_4.0.5            igraph_1.2.9           GenomeInfoDbData_1.2.4
 [37] gtable_0.3.0           glue_1.5.0             RANN_2.6.1            
 [40] scattermore_0.7        vctrs_0.3.8            nlme_3.1-153          
 [43] iterators_1.0.13       lmtest_0.9-39          stringr_1.4.0         
 [46] globals_0.14.0         mime_0.12              miniUI_0.1.1.1        
 [49] lifecycle_1.0.1        irlba_2.3.3            goftest_1.2-3         
 [52] future_1.23.0          zlibbioc_1.36.0        MASS_7.3-54           
 [55] zoo_1.8-9              scales_1.1.1           spatstat.core_2.3-2   
 [58] promises_1.2.0.1       spatstat.utils_2.2-0   reticulate_1.22       
 [61] pbapply_1.5-0          gridExtra_2.3          rpart_4.1-15          
 [64] stringi_1.7.6          repr_1.1.3             bitops_1.0-7          
 [67] rlang_0.4.12           pkgconfig_2.0.3        evaluate_0.14         
 [70] lattice_0.20-45        ROCR_1.0-11            purrr_0.3.4           
 [73] tensor_1.5             patchwork_1.1.1        htmlwidgets_1.5.4     
 [76] cowplot_1.1.1          tidyselect_1.1.1       parallelly_1.29.0     
 [79] RcppAnnoy_0.0.19       plyr_1.8.6             magrittr_2.0.1        
 [82] R6_2.5.1               generics_0.1.1         DelayedArray_0.16.3   
 [85] pbdZMQ_0.3-6           pillar_1.6.4           withr_2.4.2           
 [88] mgcv_1.8-38            fitdistrplus_1.1-6     RCurl_1.98-1.5        
 [91] survival_3.2-13        abind_1.4-5            tibble_3.1.6          
 [94] future.apply_1.8.1     crayon_1.4.2           uuid_1.0-3            
 [97] KernSmooth_2.23-20     utf8_1.2.2             spatstat.geom_2.3-0   
[100] plotly_4.10.0          grid_4.0.5             data.table_1.14.2     
[103] digest_0.6.28          xtable_1.8-4           tidyr_1.1.4           
[106] httpuv_1.6.3           munsell_0.5.0          viridisLite_0.4.0