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Error in loadNamespace(name): there is no package called BiocInstaller #40

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moldach opened this issue Oct 29, 2019 · 0 comments
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@moldach
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moldach commented Oct 29, 2019

I'm getting an error when trying to look up some functions from the scater Bioconductor package. It's giving me an error about BiocInstaller which shouldn't be an issue since that's been replaced with BiocManager:

lookup::lookup(scater::calculateQCMetrics)

Error in loadNamespace(name) : there is no package called ‘BiocInstaller’

sessionInfo():

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /home/tsundoku/anaconda3/lib/libmkl_rt.so

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8   
 [6] LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] scater_1.12.2               SingleCellExperiment_1.6.0  SummarizedExperiment_1.14.1 DelayedArray_0.10.0         BiocParallel_1.18.1        
 [6] matrixStats_0.55.0          Biobase_2.44.0              GenomicRanges_1.36.1        GenomeInfoDb_1.20.0         IRanges_2.18.3             
[11] S4Vectors_0.22.1            BiocGenerics_0.30.0         ggplot2_3.2.1               rlang_0.4.1                 lookup_0.0.0.9000          
[16] Seurat_3.1.1                dplyr_0.8.3                

loaded via a namespace (and not attached):
  [1] ggbeeswarm_0.6.0         Rtsne_0.15               colorspace_1.4-1         ggridges_0.5.1           XVector_0.24.0           BiocNeighbors_1.2.0     
  [7] rstudioapi_0.10          leiden_0.3.1             listenv_0.7.0            npsurv_0.4-0             ggrepel_0.8.1            codetools_0.2-16        
 [13] splines_3.6.1            R.methodsS3_1.7.1        lsei_1.2-0               zeallot_0.1.0            jsonlite_1.6             ica_1.0-2               
 [19] cluster_2.1.0            png_0.1-7                R.oo_1.22.0              uwot_0.1.4               sctransform_0.2.0        BiocManager_1.30.9      
 [25] compiler_3.6.1           httr_1.4.1               backports_1.1.5          assertthat_0.2.1         Matrix_1.2-17            lazyeval_0.2.2          
 [31] BiocSingular_1.0.0       htmltools_0.4.0          tools_3.6.1              rsvd_1.0.2               igraph_1.2.4.1           gtable_0.3.0            
 [37] glue_1.3.1               GenomeInfoDbData_1.2.1   RANN_2.6.1               reshape2_1.4.3           Rcpp_1.0.2               vctrs_0.2.0             
 [43] gdata_2.18.0             ape_5.3                  nlme_3.1-141             DelayedMatrixStats_1.6.1 gbRd_0.4-11              lmtest_0.9-37           
 [49] stringr_1.4.0            globals_0.12.4           lifecycle_0.1.0          irlba_2.3.3              gtools_3.8.1             future_1.14.0           
 [55] MASS_7.3-51.4            zlibbioc_1.30.0          zoo_1.8-6                scales_1.0.0             RColorBrewer_1.1-2       memoise_1.1.0.9000      
 [61] reticulate_1.13          pbapply_1.4-2            gridExtra_2.3            stringi_1.4.3            highlite_0.0.0.9000      caTools_1.17.1.2        
 [67] bibtex_0.4.2             Rdpack_0.11-0            SDMTools_1.1-221.1       pkgconfig_2.0.3          bitops_1.0-6             lattice_0.20-38         
 [73] ROCR_1.0-7               purrr_0.3.3              htmlwidgets_1.5.1        labeling_0.3             cowplot_1.0.0            tidyselect_0.2.5        
 [79] RcppAnnoy_0.0.13         plyr_1.8.4               magrittr_1.5             R6_2.4.0                 gplots_3.0.1.1           pillar_1.4.2            
 [85] withr_2.1.2              fitdistrplus_1.0-14      survival_2.44-1.1        RCurl_1.95-4.12          tibble_2.1.3             future.apply_1.3.0      
 [91] tsne_0.1-3               crayon_1.3.4             KernSmooth_2.23-16       plotly_4.9.0             viridis_0.5.1            grid_3.6.1              
 [97] data.table_1.12.6        metap_1.1                digest_0.6.22            tidyr_1.0.0              R.utils_2.9.0            RcppParallel_4.4.4      
[103] munsell_0.5.0            beeswarm_0.2.3           viridisLite_0.3.0        vipor_0.4.5  
@jimhester jimhester added the bug label Oct 29, 2019
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