Question

DB file sqlite not found

0

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rama.pranadi • 0

@ramapranadi-22768

Last seen 4.8 years ago

Hi,

I am receiving this error when trying to use tximeta():

> se <- tximeta(coldata)
importing quantifications
reading in files with read_tsv
1 2 3 
found matching transcriptome:
[ GENCODE - Mus musculus - release M24 ]
loading existing TxDb created: 2020-01-26 06:20:01
Error in dbFileConnect(file) : 
  DB file '/Users/ramapranadinata/Library/Caches/BiocFileCache/291456c9cd_291456c9cd.sqlite' not found

is it supposed to find the BiocFileCache.sqlite file?

Thanks!

-------------------------------
Traceback()

> traceback()
5: stop("DB file '", dbfile, "' not found")
4: dbFileConnect(file)
3: loadDb(loadpath)
2: getTxDb(txomeInfo)
1: tximeta(coldata)

sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] AnnotationHub_2.18.0        BiocFileCache_1.10.2       
 [3] dbplyr_1.4.2                tximeta_1.4.3              
 [5] pheatmap_1.0.12             RColorBrewer_1.1-2         
 [7] DESeq2_1.26.0               SummarizedExperiment_1.16.1
 [9] DelayedArray_0.12.2         BiocParallel_1.20.1        
[11] matrixStats_0.55.0          Biobase_2.46.0             
[13] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
[15] IRanges_2.20.2              S4Vectors_0.24.3           
[17] BiocGenerics_0.32.0         forcats_0.4.0              
[19] stringr_1.4.0               dplyr_0.8.3                
[21] purrr_0.3.3                 readr_1.3.1                
[23] tidyr_1.0.2                 tibble_2.1.3               
[25] ggplot2_3.2.1               tidyverse_1.3.0            
[27] tximport_1.14.0             tximportData_1.14.0        

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1             
  [2] htmlTable_1.13.3             
  [3] XVector_0.26.0               
  [4] base64enc_0.1-3              
  [5] fs_1.3.1                     
  [6] rstudioapi_0.10              
  [7] bit64_0.9-7                  
  [8] interactiveDisplayBase_1.24.0
  [9] AnnotationDbi_1.48.0         
 [10] fansi_0.4.1                  
 [11] lubridate_1.7.4              
 [12] xml2_1.2.2                   
 [13] splines_3.6.2                
 [14] geneplotter_1.64.0           
 [15] knitr_1.27                   
 [16] Formula_1.2-3                
 [17] jsonlite_1.6                 
 [18] Rsamtools_2.2.1              
 [19] broom_0.5.3                  
 [20] annotate_1.64.0              
 [21] cluster_2.1.0                
 [22] png_0.1-7                    
 [23] shiny_1.4.0                  
 [24] BiocManager_1.30.10          
 [25] compiler_3.6.2               
 [26] httr_1.4.1                   
 [27] backports_1.1.5              
 [28] fastmap_1.0.1                
 [29] assertthat_0.2.1             
 [30] Matrix_1.2-18                
 [31] lazyeval_0.2.2               
 [32] cli_2.0.1                    
 [33] later_1.0.0                  
 [34] prettyunits_1.1.1            
 [35] acepack_1.4.1                
 [36] htmltools_0.4.0              
 [37] tools_3.6.2                  
 [38] gtable_0.3.0                 
 [39] glue_1.3.1                   
 [40] GenomeInfoDbData_1.2.2       
 [41] rappdirs_0.3.1               
 [42] Rcpp_1.0.3                   
 [43] cellranger_1.1.0             
 [44] vctrs_0.2.2                  
 [45] Biostrings_2.54.0            
 [46] nlme_3.1-143                 
 [47] rtracklayer_1.46.0           
 [48] xfun_0.12                    
 [49] rvest_0.3.5                  
 [50] mime_0.8                     
 [51] lifecycle_0.1.0              
 [52] ensembldb_2.10.2             
 [53] XML_3.99-0.3                 
 [54] zlibbioc_1.32.0              
 [55] scales_1.1.0                 
 [56] promises_1.1.0               
 [57] ProtGenerics_1.18.0          
 [58] hms_0.5.3                    
 [59] AnnotationFilter_1.10.0      
 [60] yaml_2.2.0                   
 [61] curl_4.3                     
 [62] memoise_1.1.0                
 [63] gridExtra_2.3                
 [64] biomaRt_2.42.0               
 [65] rpart_4.1-15                 
 [66] latticeExtra_0.6-29          
 [67] stringi_1.4.5                
 [68] RSQLite_2.2.0                
 [69] BiocVersion_3.10.1           
 [70] genefilter_1.68.0            
 [71] checkmate_1.9.4              
 [72] GenomicFeatures_1.38.1       
 [73] rlang_0.4.3                  
 [74] pkgconfig_2.0.3              
 [75] bitops_1.0-6                 
 [76] lattice_0.20-38              
 [77] GenomicAlignments_1.22.1     
 [78] htmlwidgets_1.5.1            
 [79] bit_1.1-15.1                 
 [80] tidyselect_0.2.5             
 [81] magrittr_1.5                 
 [82] R6_2.4.1                     
 [83] generics_0.0.2               
 [84] Hmisc_4.3-0                  
 [85] DBI_1.1.0                    
 [86] pillar_1.4.3                 
 [87] haven_2.2.0                  
 [88] foreign_0.8-75               
 [89] withr_2.1.2                  
 [90] survival_3.1-8               
 [91] RCurl_1.98-1.1               
 [92] nnet_7.3-12                  
 [93] modelr_0.1.5                 
 [94] crayon_1.3.4                 
 [95] progress_1.2.2               
 [96] jpeg_0.1-8.1                 
 [97] locfit_1.5-9.1               
 [98] grid_3.6.2                   
 [99] readxl_1.3.1                 
[100] data.table_1.12.8            
[101] blob_1.2.1                   
[102] reprex_0.3.0                 
[103] digest_0.6.23                
[104] xtable_1.8-4                 
[105] httpuv_1.5.2                 
[106] openssl_1.4.1                
[107] munsell_0.5.0                
[108] askpass_1.1

tximeta sqlite • 2.1k views

ADD COMMENT • link updated 4.8 years ago by Martin Morgan 25k • written 4.8 years ago by rama.pranadi • 0

0

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Just to be clear, you should use bfcremove() to remove the entry, not removing any files manually.

ADD REPLY • link 4.8 years ago Michael Love 43k

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Entering edit mode

Thank you for the prompt response Michael. I am trying to download the BioFileCache package and run into this error. This was a pretty large error message so I hope what I provided is enough. Many thanks in advance for any help on this as well!

> BiocManager::install("BiocFileCache")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'BiocFileCache'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/3.6/BiocFileCache_1.10.2.tgz'
Content type 'application/x-gzip' length 464311 bytes (453 KB)
==================================================
downloaded 453 KB


The downloaded binary packages are in
    /var/folders/2n/gg0vsfs11vdbh_hrlcqstr4w0000gn/T//Rtmpm61zmE/downloaded_packages
Old packages: 'RcppArmadillo'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
                   binary      source needs_compilation
RcppArmadillo 0.9.800.3.0 0.9.800.4.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package 'RcppArmadillo'

trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.9.800.4.0.tar.gz'
Content type 'application/x-gzip' length 1374219 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

...
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo’

The downloaded source packages are in
    '/private/var/folders/2n/gg0vsfs11vdbh_hrlcqstr4w0000gn/T/Rtmpm61zmE/downloaded_packages'
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package 'RcppArmadillo' had non-zero exit status

ADD REPLY • link updated 4.8 years ago by Martin Morgan 25k • written 4.8 years ago by rama.pranadi • 0

0

Entering edit mode

Ive actually been having the same problem when trying to install 'mygene' and 'annotate' packages. E.g. Error from trying to install mygene package (see below).

Error:

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo’

The downloaded source packages are in
    '/private/var/folders/2n/gg0vsfs11vdbh_hrlcqstr4w0000gn/T/Rtmpm61zmE/downloaded_packages'
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package 'RcppArmadillo' had non-zero exit status

ADD REPLY • link updated 4.8 years ago by Martin Morgan 25k • written 4.8 years ago by rama.pranadi • 0

0

Entering edit mode

For one thing, tximeta depends on BiocFileCache so you shouldn’t need to re-install. It cannot install without BFC.

Also, you genetally can say “no” to build from source.

ADD REPLY • link 4.8 years ago Michael Love 43k

0

Entering edit mode

Thank you so much for the guidance/help. All fixed!

Regards, Rama

ADD REPLY • link 4.8 years ago rama.pranadi • 0

score 0 · Answer 1 · 2020-01-26

What happened here is that the package built a database and stored it in the file cache, but then that database was wiped out somehow. The solution would be to remove the entry from the file cache, so tximeta will rebuild the database. Tximeta uses the standard BiocFileCache location so check out that package vignette (BFC) for how to remove an entry. The entry to remove is labelled by the GTF filename.