############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:ensembldb.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings ensembldb_2.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ensembldb/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ensembldb’ version ‘2.31.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ensembldb’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: EnsDb-exonsBy.Rd: supportedFilters, GRangesFilter EnsDb-sequences.Rd: TwoBitFile-class Filter-classes.Rd: AnnotationFilter, supportedFilters, GeneIdFilter ProteinFunctionality.Rd: supportedFilters proteinToTranscript.Rd: fiveUTRsByTranscript Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ensembldb-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: select > ### Title: Integration into the AnnotationDbi framework > ### Aliases: select select,EnsDb-method columns,EnsDb-method > ### keys,EnsDb-method keytypes,EnsDb-method mapIds,EnsDb-method > ### Keywords: classes > > ### ** Examples > > > library(EnsDb.Hsapiens.v86) > edb <- EnsDb.Hsapiens.v86 > > ## List all supported keytypes. > keytypes(edb) [1] "ENTREZID" "EXONID" "GENEBIOTYPE" [4] "GENEID" "GENENAME" "PROTDOMID" [7] "PROTEINDOMAINID" "PROTEINDOMAINSOURCE" "PROTEINID" [10] "SEQNAME" "SEQSTRAND" "SYMBOL" [13] "TXBIOTYPE" "TXID" "TXNAME" [16] "UNIPROTID" > > ## List all supported columns for the select and mapIds methods. > columns(edb) [1] "ENTREZID" "EXONID" "EXONIDX" [4] "EXONSEQEND" "EXONSEQSTART" "GENEBIOTYPE" [7] "GENEID" "GENENAME" "GENESEQEND" [10] "GENESEQSTART" "INTERPROACCESSION" "ISCIRCULAR" [13] "PROTDOMEND" "PROTDOMSTART" "PROTEINDOMAINID" [16] "PROTEINDOMAINSOURCE" "PROTEINID" "PROTEINSEQUENCE" [19] "SEQCOORDSYSTEM" "SEQLENGTH" "SEQNAME" [22] "SEQSTRAND" "SYMBOL" "TXBIOTYPE" [25] "TXCDSSEQEND" "TXCDSSEQSTART" "TXID" [28] "TXNAME" "TXSEQEND" "TXSEQSTART" [31] "UNIPROTDB" "UNIPROTID" "UNIPROTMAPPINGTYPE" > > ## List /real/ database column names. > listColumns(edb) [1] "seq_name" "seq_length" "is_circular" [4] "gene_id" "entrezid" "exon_id" [7] "exon_seq_start" "exon_seq_end" "gene_name" [10] "gene_biotype" "gene_seq_start" "gene_seq_end" [13] "seq_strand" "seq_coord_system" "symbol" [16] "tx_id" "protein_id" "protein_sequence" [19] "protein_domain_id" "protein_domain_source" "interpro_accession" [22] "prot_dom_start" "prot_dom_end" "tx_biotype" [25] "tx_seq_start" "tx_seq_end" "tx_cds_seq_start" [28] "tx_cds_seq_end" "tx_name" "exon_idx" [31] "uniprot_id" "uniprot_db" "uniprot_mapping_type" > > ## Retrieve all keys corresponding to transcript ids. > txids <- keys(edb, keytype = "TXID") > length(txids) [1] 216741 > head(txids) [1] "ENST00000000233" "ENST00000000412" "ENST00000000442" "ENST00000001008" [5] "ENST00000001146" "ENST00000002125" > > ## Retrieve all keys corresponding to gene names of genes encoded on chromosome X > gids <- keys(edb, keytype = "GENENAME", filter = SeqNameFilter("X")) > length(gids) [1] 2300 > head(gids) [1] "TSPAN6" "TNMD" "LAS1L" "CD99" "KLHL13" "ARX" > > ## Get a mapping of the genes BCL2 and BCL2L11 to all of their > ## transcript ids and return the result as list > maps <- mapIds(edb, keys = c("BCL2", "BCL2L11"), column = "TXID", + keytype = "GENENAME", multiVals = "list") > maps $BCL2 [1] "ENST00000398117" "ENST00000333681" "ENST00000590515" "ENST00000589955" $BCL2L11 [1] "ENST00000432179" "ENST00000308659" "ENST00000393256" "ENST00000393252" [5] "ENST00000433098" "ENST00000405953" "ENST00000415458" "ENST00000436733" [9] "ENST00000437029" "ENST00000452231" "ENST00000361493" "ENST00000431217" [13] "ENST00000439718" "ENST00000438054" "ENST00000337565" "ENST00000622509" [17] "ENST00000619294" "ENST00000610735" "ENST00000622612" "ENST00000357757" [21] "ENST00000615946" "ENST00000621302" "ENST00000620862" "LRG_620t1" [25] "LRG_620t2" "LRG_620t3" "LRG_620t4" "LRG_620t5" > > ## Perform the same query using a combination of a GeneNameFilter and a > ## TxBiotypeFilter to just retrieve protein coding transcripts for these > ## two genes. > mapIds(edb, keys = list(GeneNameFilter(c("BCL2", "BCL2L11")), + TxBiotypeFilter("protein_coding")), column = "TXID", + multiVals = "list") Warning in .mapIds(x = x, keys = keys, column = column, keytype = keytype, : Got 2 filter objects. Will use the keys of the first for the mapping! Note: ordering of the results might not match ordering of keys! $BCL2 [1] "ENST00000398117" "ENST00000333681" "ENST00000589955" $BCL2L11 [1] "ENST00000432179" "ENST00000308659" "ENST00000393256" "ENST00000393252" [5] "ENST00000405953" "ENST00000438054" "ENST00000337565" "ENST00000622509" [9] "ENST00000619294" "ENST00000610735" "ENST00000622612" "ENST00000357757" [13] "ENST00000615946" "ENST00000621302" "ENST00000620862" > > ## select: > ## Retrieve all transcript and gene related information for the above example. > select(edb, keys = list(GeneNameFilter(c("BCL2", "BCL2L11")), + TxBiotypeFilter("protein_coding")), + columns = c("GENEID", "GENENAME", "TXID", "TXBIOTYPE", "TXSEQSTART", + "TXSEQEND", "SEQNAME", "SEQSTRAND")) Note: ordering of the results might not match ordering of keys! GENEID GENENAME TXID TXBIOTYPE TXSEQSTART TXSEQEND 1 ENSG00000171791 BCL2 ENST00000398117 protein_coding 63123346 63320128 2 ENSG00000171791 BCL2 ENST00000333681 protein_coding 63127035 63319786 3 ENSG00000171791 BCL2 ENST00000589955 protein_coding 63313802 63318812 4 ENSG00000153094 BCL2L11 ENST00000432179 protein_coding 111119378 111124112 5 ENSG00000153094 BCL2L11 ENST00000308659 protein_coding 111120914 111165048 6 ENSG00000153094 BCL2L11 ENST00000393256 protein_coding 111120929 111168447 7 ENSG00000153094 BCL2L11 ENST00000393252 protein_coding 111122670 111123960 8 ENSG00000153094 BCL2L11 ENST00000405953 protein_coding 111123746 111128837 9 ENSG00000153094 BCL2L11 ENST00000438054 protein_coding 111123752 111146284 10 ENSG00000153094 BCL2L11 ENST00000337565 protein_coding 111120914 111128844 11 ENSG00000153094 BCL2L11 ENST00000622509 protein_coding 111120914 111168445 12 ENSG00000153094 BCL2L11 ENST00000619294 protein_coding 111120914 111168445 13 ENSG00000153094 BCL2L11 ENST00000610735 protein_coding 111120914 111168445 14 ENSG00000153094 BCL2L11 ENST00000622612 protein_coding 111120914 111168445 15 ENSG00000153094 BCL2L11 ENST00000357757 protein_coding 111120914 111146281 16 ENSG00000153094 BCL2L11 ENST00000615946 protein_coding 111120914 111168445 17 ENSG00000153094 BCL2L11 ENST00000621302 protein_coding 111120914 111168445 18 ENSG00000153094 BCL2L11 ENST00000620862 protein_coding 111120914 111168445 SEQNAME SEQSTRAND 1 18 -1 2 18 -1 3 18 -1 4 2 1 5 2 1 6 2 1 7 2 1 8 2 1 9 2 1 10 2 1 11 2 1 12 2 1 13 2 1 14 2 1 15 2 1 16 2 1 17 2 1 18 2 1 > > ## Get all data for genes encoded on chromosome Y > Y <- select(edb, keys = "Y", keytype = "SEQNAME") Error: database or disk is full Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 7. └─ensembldb (local) .local(x, ...) 8. └─ensembldb:::.getWhat(...) 9. ├─DBI::dbGetQuery(dbconn(x), Q) 10. └─DBI::dbGetQuery(dbconn(x), Q) 11. └─DBI (local) .local(conn, statement, ...) 12. ├─DBI::dbFetch(rs, n = n, ...) 13. └─RSQLite::dbFetch(rs, n = n, ...) 14. └─RSQLite (local) .local(res, n, ...) 15. └─RSQLite:::result_fetch(res@ptr, n = n) [ FAIL 7 | WARN 75 | SKIP 3 | PASS 1517 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/00check.log’ for details.