Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() when finished working with a connection
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Entering edit mode
@nikolay-ivanov-23079
Last seen 11 weeks ago
USA/New York City/Weill Cornell Medicine

I have noticed that after I run tximeta's summarizeToGene function, I get the following warning:

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

If I execute the same command the second time, I do not get a warning.

What does the warning mean? Will it affect my analysis?

Thank you!


library(DESeq2)
library(tximeta)

# import data
se = tximeta(coldata = dataset_metadata, type = "salmon")

# summarize transcript-level quantifications to gene-level
gse = summarizeToGene(se)
loading existing EnsDb created: 2021-02-25 02:40:59
obtaining transcript-to-gene mapping from database
loading existing gene ranges created: 2021-02-25 02:52:08
summarizing abundance
summarizing counts
summarizing length
Warning message:
call dbDisconnect() when finished working with a connection

# execute the command again
gse = summarizeToGene(se)
loading existing EnsDb created: 2021-02-25 02:40:59
obtaining transcript-to-gene mapping from database
loading existing gene ranges created: 2021-02-25 02:52:08
summarizing abundance
summarizing counts
summarizing length

# no warning message this time around

sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /pbtech_mounts/homes027/nai2008/anaconda3/envs/R_4.0/lib/libopenblasp-r0.3.10.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] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] tximeta_1.8.4               DESeq2_1.30.0
 [3] SummarizedExperiment_1.20.0 Biobase_2.50.0
 [5] MatrixGenerics_1.2.0        matrixStats_0.58.0
 [7] GenomicRanges_1.42.0        GenomeInfoDb_1.26.0
 [9] IRanges_2.24.0              S4Vectors_0.28.0
[11] BiocGenerics_0.36.0

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.22.0           bitops_1.0-6
 [3] bit64_4.0.5                   RColorBrewer_1.1-2
 [5] progress_1.2.2                httr_1.4.2
 [7] tools_4.0.3                   R6_2.5.0
 [9] DBI_1.1.1                     lazyeval_0.2.2
[11] colorspace_2.0-0              withr_2.4.1
[13] tidyselect_1.1.0              prettyunits_1.1.1
[15] bit_4.0.4                     curl_4.3
[17] compiler_4.0.3                xml2_1.3.2
[19] DelayedArray_0.16.0           rtracklayer_1.50.0
[21] scales_1.1.1                  readr_1.4.0
[23] genefilter_1.72.0             askpass_1.1
[25] rappdirs_0.3.1                stringr_1.4.0
[27] digest_0.6.27                 Rsamtools_2.6.0
[29] XVector_0.30.0                pkgconfig_2.0.3
[31] htmltools_0.5.1.1             dbplyr_2.0.0
[33] fastmap_1.1.0                 ensembldb_2.14.0
[35] rlang_0.4.10                  rstudioapi_0.13
[37] RSQLite_2.2.3                 shiny_1.6.0
[39] generics_0.1.0                jsonlite_1.7.2
[41] BiocParallel_1.24.0           dplyr_1.0.4
[43] RCurl_1.98-1.2                magrittr_2.0.1
[45] GenomeInfoDbData_1.2.4        Matrix_1.3-2
[47] Rcpp_1.0.6                    munsell_0.5.0
[49] lifecycle_0.2.0               stringi_1.5.3
[51] yaml_2.2.1                    zlibbioc_1.36.0
[53] BiocFileCache_1.14.0          AnnotationHub_2.22.0
[55] grid_4.0.3                    blob_1.2.1
[57] promises_1.1.1                crayon_1.4.1
[59] lattice_0.20-41               Biostrings_2.58.0
[61] splines_4.0.3                 GenomicFeatures_1.42.1
[63] annotate_1.68.0               hms_1.0.0
[65] locfit_1.5-9.4                pillar_1.4.7
[67] geneplotter_1.68.0            biomaRt_2.46.1
[69] XML_3.99-0.5                  glue_1.4.2
[71] BiocVersion_3.12.0            BiocManager_1.30.10
[73] vctrs_0.3.6                   httpuv_1.5.5
[75] gtable_0.3.0                  openssl_1.4.3
[77] purrr_0.3.4                   assertthat_0.2.1
[79] cachem_1.0.3                  ggplot2_3.3.3
[81] mime_0.9                      xtable_1.8-4
[83] AnnotationFilter_1.14.0       later_1.1.0.1
[85] survival_3.2-7                tibble_3.0.6
[87] GenomicAlignments_1.26.0      AnnotationDbi_1.52.0
[89] memoise_2.0.0                 tximport_1.18.0
[91] ellipsis_0.3.1                interactiveDisplayBase_1.28.0
tximeta • 187 views
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1
Entering edit mode
@mikelove
Last seen 4 hours ago
United States

This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.

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