Warning: call dbDisconnect() when finished working with a connection #15
Description
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