Cannot install clusterProfiler
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dtatarak • 0
@dtatarak-15870
Last seen 5.9 years ago

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!

clusterprofiler biocinstaller • 8.9k views
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@james-w-macdonald-5106
Last seen 30 minutes ago
United States

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.

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I tried that. It installs successfully, but I still get the exact same error when installing clusterProfiler.

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Then install bit using biocLite

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 days ago
China/Guangzhou/Southern Medical Univer…
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thkapell ▴ 10
@tkapell-14647
Last seen 14 months ago
Helmholtz Center Munich, Germany

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

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