Problem using biomaRt

Question

[biomagician]

Hi,

This code used to work for me but it's not working anymore:

ensembl <- biomaRt::useMart('ensembl', dataset = 'celegans_gene_ensembl')
restarting interrupted promise evaluationinternal error -3 in R_decompress1Error in biomaRt::useMart("ensembl", dataset = "celegans_gene_ensembl") : 
  lazy-load database '/usr/local/lib/R/3.4/site-library/biomaRt/R/biomaRt.rdb' is corrupt

Can somebody help me, please?

My session info:

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin16.5.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

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

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

other attached packages:
[1] ALL_1.18.0           IRanges_2.10.2       S4Vectors_0.14.3    
[4] Biobase_2.36.2       graph_1.54.0         BiocGenerics_0.22.0 
[7] BiocInstaller_1.26.0 bindrcpp_0.2         dplyr_0.7.2         

loaded via a namespace (and not attached):
  [1] TH.data_1.0-8              colorspace_1.3-2          
  [3] seqinr_3.4-5               rprojroot_1.2             
  [5] htmlTable_1.9              XVector_0.16.0            
  [7] GenomicRanges_1.28.4       base64enc_0.1-3           
  [9] topGO_2.28.0               bit64_0.9-7               
 [11] AnnotationDbi_1.38.2       mvtnorm_1.0-6             
 [13] codetools_0.2-15           splines_3.4.0             
 [15] tximport_1.4.0             doBy_4.5-15               
 [17] geneplotter_1.54.0         knitr_1.16                
 [19] ade4_1.7-6                 Formula_1.2-2             
 [21] jsonlite_1.5               Rsamtools_1.28.0          
 [23] annotate_1.54.0            GO.db_3.4.1               
 [25] cluster_2.0.6              pheatmap_1.0.8            
 [27] compiler_3.4.0             backports_1.1.0           
 [29] assertthat_0.2.0           Matrix_1.2-10             
 [31] lazyeval_0.2.0             acepack_1.4.1             
 [33] htmltools_0.3.6            tools_3.4.0               
 [35] gtable_0.2.0               glue_1.1.1                
 [37] GenomeInfoDbData_0.99.0    Rcpp_0.12.12              
 [39] Biostrings_2.44.2          ape_4.1                   
 [41] nlme_3.1-131               rtracklayer_1.36.4        
 [43] pinfsc50_1.1.0             refGenome_1.7.3           
 [45] stringr_1.2.0              network_1.13.0            
 [47] devtools_1.13.3            XML_3.98-1.9              
 [49] zlibbioc_1.22.0            MASS_7.3-47               
 [51] zoo_1.8-0                  scales_0.4.1              
 [53] microbenchmark_1.4-2.1     BSgenome_1.44.0           
 [55] VariantAnnotation_1.22.3   SummarizedExperiment_1.6.3
 [57] sandwich_2.4-0             SparseM_1.77              
 [59] RColorBrewer_1.1-2         yaml_2.1.14               
 [61] memoise_1.1.0              gridExtra_2.2.1           
 [63] ggplot2_2.2.1              biomaRt_2.32.1            
 [65] rpart_4.1-11               latticeExtra_0.6-28       
 [67] stringi_1.1.5              RSQLite_2.0               
 [69] genefilter_1.58.1          checkmate_1.8.3           
 [71] permute_0.9-4              GenomicFeatures_1.28.4    
 [73] BiocParallel_1.10.1        GenomeInfoDb_1.12.2       
 [75] rlang_0.1.1                pkgconfig_2.0.1           
 [77] matrixStats_0.52.2         bitops_1.0-6              
 [79] evaluate_0.10.1            lattice_0.20-35           
 [81] bindr_0.1                  GenomicAlignments_1.12.1  
 [83] htmlwidgets_0.9            labeling_0.3              
 [85] bit_1.1-12                 plyr_1.8.4                
 [87] magrittr_1.5               DESeq2_1.16.1             
 [89] R6_2.2.2                   Hmisc_4.0-3               
 [91] multcomp_1.4-6             DelayedArray_0.2.7        
 [93] DBI_0.7                    foreign_0.8-69            
 [95] withr_2.0.0                mgcv_1.8-18               
 [97] survival_2.41-3            RCurl_1.95-4.8            
 [99] nnet_7.3-12                tibble_1.3.3              
[101] vcfR_1.5.0                 rmarkdown_1.6             
[103] locfit_1.5-9.1             grid_3.4.0                
[105] data.table_1.10.4          blob_1.1.0                
[107] vegan_2.4-3                digest_0.6.12             
[109] xtable_1.8-2               munsell_0.4.3             
[111] viridisLite_0.2.0          gsalib_2.1

Thanks. Best wishes, C.

[Jean-Karim Heriche]

This looks like a problem with the package installation. Remove it and try to install it again.

[biomagician]

Do you know how?

[biomagician]

I did this:

Quit your R session
Start a new session with R --vanilla
Run the command remove.packages("BiocInstaller")
Repeat that command until R says there is no such package.
Run the command source("https://bioconductor.org/biocLite.R")
Run biocValid() to ensure your installed packages are valid for the current version of Bioconductor, and follow the instructions it gives you.

as suggested here: https://www.bioconductor.org/install/ and it worked. Fantastic, thanks!

Answer 1

[biomagician]

I did this:

Quit your R session
Start a new session with R --vanilla
Run the command remove.packages("BiocInstaller")
Repeat that command until R says there is no such package.
Run the command source("https://bioconductor.org/biocLite.R")
Run biocValid() to ensure your installed packages are valid for the current version of Bioconductor, and follow the instructions it gives you.

as suggested here: https://www.bioconductor.org/install/ and it worked. Fantastic, thanks!