Warning: call dbDisconnect() when finished working with a connection
dariomel opened this issue · comments
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
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).
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.