PLEASE HELP for " Error in rsqlite_send_query(conn@ptr, statement) : external pointer is not valid"
1
0
Entering edit mode
4.2 years ago

Hi,

I am trying to convert a list of ensembl ids to entrez ids by using "org.Hs.eg.db" package and I receive the following error:

library(org.Hs.eg.db)

de_genes_entrez_ids = mapIds(org.Hs.eg.db, de_genes ,column="ENTREZID", keytype="ENSEMBL", multiVals="first")

Error in rsqlite_send_query(conn@ptr, statement) : external pointer is not valid

I am a beginner in R enviroment so any help would be really appreciated. I tried to remove and install R but it did not work. I come across same error both in Windows 10 and Ubuntu 16.04 LTS.

Edit: I recognized that I receive this error for almost any package I try to use now. I just happened to see this error since yesterday.

Edit2: I included the traceback().

Thanks,

Yusuf Kazci

traceback()

20: stop(list(message = "external pointer is not valid", call = rsqlite_send_query(conn@ptr,

    statement), cppstack = list(file = "", line = -1L, stack = "C++ stack not available on this system")))

19: .Call(RSQLite_rsqlite_send_query, con, sql)

18: rsqlite_send_query(conn@ptr, statement)

17: initialize(value, ...)

16: initialize(value, ...)

15: new("SQLiteResult", sql = statement, ptr = rsqlite_send_query(conn@ptr,

    statement), conn = conn)

14: .local(conn, statement, ...)

13: dbSendQuery(conn, statement, ...)

12: dbSendQuery(conn, statement, ...)

11: .local(conn, statement, ...)

10: dbGetQuery(conn, SQL)

9: dbGetQuery(conn, SQL)

8: dbQuery(dbconn(x), "SELECT value FROM metadata WHERE name='CENTRALID'")

7: .getCentralID(x)

6: .chooseJoinType(x)

5: select(x, keys = unique(keys), columns = column, keytype = keytype)

4: select(x, keys = unique(keys), columns = column, keytype = keytype)

3: mapIds_base(x, keys, column, keytype, ..., multiVals = multiVals)

2: mapIds(org.Hs.eg.db, keys = de.genes_up_in_ccm2_vs_ccm1, column = "ENTREZID",

   keytype = "ENSEMBL", multiVals = "first")

1: mapIds(org.Hs.eg.db, keys = de.genes_up_in_ccm2_vs_ccm1, column = "ENTREZID",

   keytype = "ENSEMBL", multiVals = "first")

sessionInfo()

R version 3.4.1 (2017-06-30)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Turkish_Turkey.1254 LC_CTYPE=Turkish_Turkey.1254
[3] LC_MONETARY=Turkish_Turkey.1254 LC_NUMERIC=C
[5] LC_TIME=Turkish_Turkey.1254

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

other attached packages: [1] DESeq2_1.16.1 SummarizedExperiment_1.6.3 DelayedArray_0.2.7
[4] matrixStats_0.52.2 GenomicRanges_1.28.4 GenomeInfoDb_1.12.2
[7] org.Hs.eg.db_3.4.1 AnnotationDbi_1.38.2 IRanges_2.10.2
[10] S4Vectors_0.14.3 Biobase_2.36.2 BiocGenerics_0.22.0

loaded via a namespace (and not attached): [1] tidyr_0.6.3 bit64_0.9-7 splines_3.4.1
[4] Formula_1.2-2 DO.db_2.9 rvcheck_0.0.9
[7] latticeExtra_0.6-28 blob_1.1.0 Rsamtools_1.28.0
[10] GenomeInfoDbData_0.99.0 RSQLite_2.0 backports_1.1.0
[13] lattice_0.20-35 digest_0.6.12 RColorBrewer_1.1-2
[16] XVector_0.16.0 checkmate_1.8.3 qvalue_2.8.0
[19] colorspace_1.3-2 htmltools_0.3.6 Matrix_1.2-10
[22] plyr_1.8.4 XML_3.98-1.9 pkgconfig_2.0.1
[25] clusterProfiler_3.4.4 biomaRt_2.32.1 genefilter_1.58.1
[28] zlibbioc_1.22.0 xtable_1.8-2 GO.db_3.4.1
[31] scales_0.4.1 BiocParallel_1.10.1 htmlTable_1.9
[34] tibble_1.3.3 annotate_1.54.0 ggplot2_2.2.1
[37] GenomicFeatures_1.28.4 nnet_7.3-12 lazyeval_0.2.0
[40] survival_2.41-3 magrittr_1.5 memoise_1.1.0
[43] DOSE_3.2.0 foreign_0.8-69 tools_3.4.1
[46] data.table_1.10.4 stringr_1.2.0 munsell_0.4.3
[49] locfit_1.5-9.1 cluster_2.0.6 Biostrings_2.44.2
[52] compiler_3.4.1 rlang_0.1.2 grid_3.4.1
[55] RCurl_1.95-4.8 htmlwidgets_0.9 igraph_1.1.2
[58] bitops_1.0-6 base64enc_0.1-3 gtable_0.2.0
[61] DBI_0.7 reshape2_1.4.2 GenomicAlignments_1.12.1 [64] gridExtra_2.2.1 rtracklayer_1.36.4 knitr_1.17
[67] bit_1.1-12 fastmatch_1.1-0 Hmisc_4.0-3
[70] fgsea_1.2.1 stringi_1.1.5 GOSemSim_2.2.0
[73] Rcpp_0.12.12 geneplotter_1.54.0 rpart_4.1-11
[76] acepack_1.4.1

RNA-Seq error org.Hs.eg.db package • 4.7k views
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Entering edit mode

Does anybody have any idea ? I have this same error in any computer I tried :(

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Entering edit mode
4.2 years ago

I think I understood the reason for the occurence of that error and although not know the underlying techniqual reason behind it ,- as a complete novice in R. For beginners who might experience same issue like me, I just realized that when I load the workspace to reach the object that contains the ensembl ids and require the "org.Hs.ens.db" package to convert to entrez ids, the following error occurs: "Error in rsqlite_send_query(conn@ptr, statement) : external pointer is not valid." .

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