biomaRt error: database disk image is malformed
Entering edit mode
Last seen 2.1 years ago

Hi ,

I have been lately running into the following issue with biomaRt. Everytime I use the useEnsembl() function, I get the error message shown below.

> ensembl <- biomaRt::useEnsembl("ensembl", dataset="mmusculus_gene_ensembl", host = "")

Error: database disk image is malformed
In addition: Warning messages:
1: Couldn't set cache size: database disk image is malformed
Use `cache_size` = NULL to turn off this warning. 
2: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning.

sessionInfo( )

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /g/easybuild/x86_64/CentOS/7/haswell/software/FlexiBLAS/3.0.4-GCC-10.3.0/lib64/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 

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

other attached packages:
 [1] DESeq2_1.33.5               SummarizedExperiment_1.23.4 Biobase_2.53.0              MatrixGenerics_1.5.4       
 [5] matrixStats_0.61.0          forcats_0.5.1               stringr_1.4.0               dplyr_1.0.7                
 [9] purrr_0.3.4                 readr_2.0.2                 tidyr_1.1.4                 tibble_3.1.5               
[13] ggplot2_3.3.5               tidyverse_1.3.1             rGREAT_1.25.2               GenomicRanges_1.45.0       
[17] GenomeInfoDb_1.29.8         IRanges_2.27.2              S4Vectors_0.31.5            BiocGenerics_0.39.2        
[21] ChIPseeker_1.29.1          

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                              tidyselect_1.1.1                       
  [3] htmlwidgets_1.5.4                       RSQLite_2.2.8                          
  [5] AnnotationDbi_1.55.1                    grid_4.1.0                             
  [7] BiocParallel_1.27.12                    devtools_2.4.2                         
  [9] scatterpie_0.1.7                        munsell_0.5.0                          
 [11] preprocessCore_1.55.2                   codetools_0.2-18                       
 [13] withr_2.4.2                             colorspace_2.0-2                       
 [15] GOSemSim_2.19.1                         filelock_1.0.2                         
 [17] knitr_1.36                              rstudioapi_0.13                        
 [19] DOSE_3.19.3                             GenomeInfoDbData_1.2.7                 
 [21] polyclip_1.10-0                         bit64_4.0.5                            
 [23] farver_2.1.0                            rprojroot_2.0.2                        
 [25] vctrs_0.3.8                             treeio_1.17.2                          
 [27] generics_0.1.0                          xfun_0.26                              
 [29] BiocFileCache_2.1.1                     fastcluster_1.2.3                      
 [31] R6_2.5.1                                doParallel_1.0.16                      
 [33] clue_0.3-59                             graphlayouts_0.7.1                     
 [35] locfit_1.5-9.4                          bitops_1.0-7                           
 [37] cachem_1.0.6                            fgsea_1.19.4                           
 [39] gridGraphics_0.5-1                      DelayedArray_0.19.4                    
 [41] csdR_0.99.8                             assertthat_0.2.1                       
 [43] BiocIO_1.3.0                            scales_1.1.1                           
 [45] nnet_7.3-16                             ggraph_2.0.5                           
 [47] enrichplot_1.13.1                       gtable_0.3.0                           
 [49] processx_3.5.2                          WGCNA_1.70-3                           
 [51] tidygraph_1.2.0                         rlang_0.4.11                           
 [53] genefilter_1.75.1                       GlobalOptions_0.1.2                    
 [55] splines_4.1.0                           rtracklayer_1.53.1                     
 [57] lazyeval_0.2.2                          impute_1.67.0                          
 [59] checkmate_2.0.0                         broom_0.7.9                            
 [61] modelr_0.1.8                            BiocManager_1.30.16                    
 [63] yaml_2.2.1                              reshape2_1.4.4                         
 [65] backports_1.2.1                         GenomicFeatures_1.45.2                 
 [67] Hmisc_4.5-0                             qvalue_2.25.0                          
 [69] usethis_2.0.1                           tools_4.1.0                            
 [71] ggplotify_0.1.0                         ellipsis_0.3.2                         
 [73] gplots_3.1.1                            RColorBrewer_1.1-2                     
 [75] dynamicTreeCut_1.63-1                   sessioninfo_1.1.1                      
 [77] Rcpp_1.0.7                              plyr_1.8.6                             
 [79] base64enc_0.1-3                         progress_1.2.2                         
 [81] zlibbioc_1.39.0                         RCurl_1.98-1.5                         
 [83] ps_1.6.0                                prettyunits_1.1.1                      
 [85] rpart_4.1-15                            GetoptLong_1.0.5                       
 [87] viridis_0.6.1                           haven_2.4.3                            
 [89] ggrepel_0.9.1                           cluster_2.1.2                          
 [91] fs_1.5.0                                magrittr_2.0.1                         
 [93] data.table_1.14.2                       DO.db_2.9                              
 [95] circlize_0.4.13                         reprex_2.0.1                           
 [97] pkgload_1.2.2                           hms_1.1.1                              
 [99] patchwork_1.1.1                         evaluate_0.14                          
[101] xtable_1.8-4                            RhpcBLASctl_0.21-247                   
[103] XML_3.99-0.8                            jpeg_0.1-9                             
[105] readxl_1.3.1                            gridExtra_2.3                          
[107] shape_1.4.6                             testthat_3.1.0                         
[109] compiler_4.1.0                          biomaRt_2.49.4                         
[111] KernSmooth_2.23-20                      crayon_1.4.1                           
[113] shadowtext_0.0.9                        htmltools_0.5.2                        
[115] tzdb_0.1.2                              ggfun_0.0.4                            
[117] Formula_1.2-4                           geneplotter_1.71.0                     
[119] aplot_0.1.1                             lubridate_1.7.10                       
[121] DBI_1.1.1                               tweenr_1.0.2                           
[123] dbplyr_2.1.1                            ComplexHeatmap_2.9.4                   
[125] MASS_7.3-54                             rappdirs_0.3.3                         
[127] boot_1.3-28                             Matrix_1.3-4                           
[129] cli_3.0.1                               parallel_4.1.0                         
[131] igraph_1.2.6                            pkgconfig_2.0.3                        
[133] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicAlignments_1.29.0               
[135] foreign_0.8-81                          xml2_1.3.2                             
[137] foreach_1.5.1                           ggtree_3.1.5                           
[139] annotate_1.71.0                         XVector_0.33.0                         
[141] rvest_1.0.1                             yulab.utils_0.0.2                      
[143] callr_3.7.0                             digest_0.6.28                          
[145] Biostrings_2.61.2                       cellranger_1.1.0                       
[147] rmarkdown_2.11                          fastmatch_1.1-3                        
[149] htmlTable_2.2.1                         tidytree_0.3.5                         
[151] restfulr_0.0.13                         curl_4.3.2                             
[153] Rsamtools_2.9.1                         gtools_3.9.2                           
[155] rjson_0.2.20                            lifecycle_1.0.1                        
[157] nlme_3.1-153                            jsonlite_1.7.2                         
[159] desc_1.4.0                              viridisLite_0.4.0                      
[161] fansi_0.5.0                             pillar_1.6.3                           
[163] lattice_0.20-45                         KEGGREST_1.33.0                        
[165] fastmap_1.1.0                           httr_1.4.2                             
[167] plotrix_3.8-2                           pkgbuild_1.2.0                         
[169] survival_3.2-13                         GO.db_3.14.0                           
[171] remotes_2.4.1                           glue_1.4.2                             
[173] png_0.1-7                               iterators_1.0.13                       
[175] bit_4.0.4                               ggforce_0.3.3                          
[177] stringi_1.7.5                           blob_1.2.2                             
[179] latticeExtra_0.6-29                     caTools_1.18.2                         
[181] memoise_2.0.0                           ape_5.5

Is there anything I could do to correct this? I'm currently unable to generate a Mart object using useEnsembl(). Curiously though, useMart() works as it should.

Thank you very much in advance!

Best, VĂ­ctor

biomaRt • 1.4k views
Entering edit mode
Last seen 30 minutes ago
United States

That looks like your cache database got corrupted somehow. You could try querying it directly to see if you get other errors, and if so just nuke it and let it get regenerated.

cache <- biomaRt:::.biomartCacheLocation()
bfc <- BiocFileCache(cache)

## or just assume it's borked and start with
## which will remove it and the next call to useEnsembl will regenerate it
Entering edit mode

Thanks James. I spoke to victorcampos1995 outside of this forum, and even those functions were throwing the same error. We established it was likely because the drive with the default cache location had run out of space, which broke any query to BiocFileCache.

The fix was to set the location of the biomaRt cache by setting the environment variable BIOMART_CACHE to a location with more space e.g.


Setting this in ~/.Rprofile ensured it was set for future R sessions too.

Entering edit mode

Ha! That was actually what I thought it was to begin with. But I know you are caching things these days, and it said 'cache', so... Anyway, glad to hear you got it sorted.

Entering edit mode

UNBORKING the bioMaRt cache biomaRt::biomartCacheClear() also fixes the troubles with PANTHER.db installation which have also something to do with "database disk image" being "malformed"

Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31)
Installing package(s) PANTHER.db
installing the source package PANTHER.db

trying URL ''

* installing *source* package PANTHER.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
Error: database disk image is malformed
Execution halted
ERROR: loading failed
In install.packages(...) :
  installation of package PANTHER.db had non-zero exit status

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