Warning: call dbDisconnect() when finished working with a connection

[dariomel]

this warning comes out in a situation that is specific to my application and is too complicated to describe and reproduce here.
However, the warning also appears when the following commands are executed immediately after starting R:

options(warn=1)
library(celldex)

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

NovershternHematopoieticData(ensembl=T)

snapshotDate(): 2021-10-19
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
snapshotDate(): 2021-10-20
loading from cache
require(“ensembldb”)
Warning: Unable to map 3426 of 13276 requested IDs.
class: SummarizedExperiment 
dim: 9850 211 
metadata(0):
assays(1): logcounts
rownames(9850): ENSG00000175899 ENSG00000128274 ... ENSG00000159840
  ENSG00000074755
rowData names(0):
colnames(211): GSM609632 GSM609633 ... GSM609841 GSM609842
colData names(3): label.main label.fine label.ont

gc()

Warning: call dbDisconnect() when finished working with a connection
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  8843461 472.3   15254835 814.7 13519245 722.1
Vcells 17372432 132.6   27509457 209.9 22857881 174.4

sessionInfo()

R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS

Matrix products: default
BLAS:   /mnt/share/apps/tools/R/R-4.1.1/lib/R/lib/libRblas.so
LAPACK: /mnt/share/apps/tools/R/R-4.1.1/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ensembldb_2.18.2            AnnotationFilter_1.18.0    
 [3] GenomicFeatures_1.46.1      AnnotationDbi_1.56.2       
 [5] celldex_1.4.0               SummarizedExperiment_1.24.0
 [7] Biobase_2.54.0              GenomicRanges_1.46.1       
 [9] GenomeInfoDb_1.30.0         IRanges_2.28.0             
[11] S4Vectors_0.32.3            BiocGenerics_0.40.0        
[13] MatrixGenerics_1.6.0        matrixStats_0.61.0         

loaded via a namespace (and not attached):
 [1] httr_1.4.2                    bit64_4.0.5                  
 [3] AnnotationHub_3.2.0           DelayedMatrixStats_1.16.0    
 [5] shiny_1.7.1                   assertthat_0.2.1             
 [7] interactiveDisplayBase_1.32.0 BiocManager_1.30.16          
 [9] BiocFileCache_2.2.0           blob_1.2.2                   
[11] Rsamtools_2.10.0              GenomeInfoDbData_1.2.7       
[13] yaml_2.2.1                    progress_1.2.2               
[15] BiocVersion_3.14.0            pillar_1.6.4                 
[17] RSQLite_2.2.8                 lattice_0.20-45              
[19] glue_1.5.1                    digest_0.6.28                
[21] promises_1.2.0.1              XVector_0.34.0               
[23] htmltools_0.5.2               httpuv_1.6.3                 
[25] Matrix_1.3-4                  XML_3.99-0.8                 
[27] pkgconfig_2.0.3               biomaRt_2.50.1               
[29] zlibbioc_1.40.0               purrr_0.3.4                  
[31] xtable_1.8-4                  later_1.3.0                  
[33] BiocParallel_1.28.1           tibble_3.1.6                 
[35] KEGGREST_1.34.0               generics_0.1.1               
[37] ellipsis_0.3.2                cachem_1.0.6                 
[39] withr_2.4.3                   lazyeval_0.2.2               
[41] magrittr_2.0.1                crayon_1.4.2                 
[43] mime_0.12                     memoise_2.0.0                
[45] fansi_0.5.0                   xml2_1.3.2                   
[47] tools_4.1.1                   prettyunits_1.1.1            
[49] hms_1.1.1                     BiocIO_1.4.0                 
[51] lifecycle_1.0.1               stringr_1.4.0                
[53] DelayedArray_0.20.0           Biostrings_2.62.0            
[55] compiler_4.1.1                rlang_0.4.12                 
[57] grid_4.1.1                    RCurl_1.98-1.5               
[59] rjson_0.2.20                  rappdirs_0.3.3               
[61] bitops_1.0-7                  ExperimentHub_2.2.0          
[63] restfulr_0.0.13               DBI_1.1.1                    
[65] curl_4.3.2                    R6_2.5.1                     
[67] GenomicAlignments_1.30.0      rtracklayer_1.54.0           
[69] dplyr_1.0.7                   fastmap_1.1.0                
[71] bit_4.0.4                     utf8_1.2.2                   
[73] filelock_1.0.2                ProtGenerics_1.26.0          
[75] stringi_1.7.5                 parallel_4.1.1               
[77] Rcpp_1.0.7                    vctrs_0.3.8                  
[79] png_0.1-7                     dbplyr_2.1.1                 
[81] tidyselect_1.1.1              sparseMatrixStats_1.6.0      

[dariomel]

note that the warning appears only the first time that the above commands are executed after starting R. Also the warning is not generated when calling NovershternHematopoieticData(ensembl=FALSE).

[LTLA]

Unlikely to be a celldex problem. Probably comes from any of the dependencies that use SQLite; best guess is that someone forgot to clean up a loose database handle. Some testing indicates that it may be some combination of ensembldb and the Hub packages, but it's hard to nail it down as both of them work fine in isolation.

I would suggest just ignoring the message.