| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-03-23 01:50 -0400 (Sun, 23 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 869 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 78/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| ensembldb 2.31.0 (landing page) Johannes Rainer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
|
To the developers/maintainers of the ensembldb package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ensembldb |
| Version: 2.31.0 |
| 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 |
| StartedAt: 2025-03-23 01:17:22 -0400 (Sun, 23 Mar 2025) |
| EndedAt: 2025-03-23 01:24:10 -0400 (Sun, 23 Mar 2025) |
| EllapsedTime: 407.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ensembldb.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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 ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking Rd \usage sections ... WARNING
Fatal error: cannot create 'R_TempDir'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Fatal error: cannot create 'R_TempDir'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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:
5. ├─ensembldb:::getWhat(...)
6. └─ensembldb:::getWhat(...)
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 21 | WARN 117 | SKIP 3 | PASS 1295 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MySQL-backend.Rmd’ using rmarkdown
--- finished re-building ‘MySQL-backend.Rmd’
--- re-building ‘coordinate-mapping-use-cases.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping-use-cases_files/figure-html/olig-plot-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping-use-cases_files/figure-html/sim2-plot-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping-use-cases_files/figure-html/ex2-plot-1.png" but not available.
--- finished re-building ‘coordinate-mapping-use-cases.Rmd’
--- re-building ‘coordinate-mapping.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping_files/figure-html/genomeToTranscript-ex1-plot-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/coordinate-mapping_files/figure-html/proteinToGenome-SYP-plot-1.png" but not available.
--- finished re-building ‘coordinate-mapping.Rmd’
--- re-building ‘ensembldb.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/vign_test/ensembldb/vignettes/ensembldb_files/figure-html/granges-zbtb16-1.png" but not available.
Quitting from ensembldb.Rmd:368-381 [example-AnnotationFilterList]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'mean': database or disk is full
---
Backtrace:
▆
1. ├─base::mean(...)
2. ├─ensembldb::lengthOf(...)
3. ├─ensembldb::lengthOf(...)
4. │ └─ensembldb (local) .local(x, ...)
5. │ ├─base::suppressWarnings(GRL <- exonsBy(x, by = of, filter = filter))
6. │ │ └─base::withCallingHandlers(...)
7. │ ├─GenomicFeatures::exonsBy(x, by = of, filter = filter)
8. │ └─ensembldb::exonsBy(x, by = of, filter = filter)
9. │ └─ensembldb (local) .local(x, by, ...)
10. │ ├─ensembldb:::getWhat(...)
11. │ └─ensembldb:::getWhat(...)
12. │ └─ensembldb (local) .local(x, ...)
13. │ └─ensembldb:::.getWhat(...)
14. │ ├─DBI::dbGetQuery(dbconn(x), Q)
15. │ └─DBI::dbGetQuery(dbconn(x), Q)
16. │ └─DBI (local) .local(conn, statement, ...)
17. │ ├─DBI::dbSendQuery(conn, statement, ...)
18. │ └─RSQLite::dbSendQuery(conn, statement, ...)
19. │ └─RSQLite (local) .local(conn, statement, ...)
20. │ ├─methods::new(...)
21. │ │ ├─methods::initialize(value, ...)
22. │ │ └─methods::initialize(value, ...)
23. │ └─RSQLite:::result_create(conn@ptr, statement)
24. └─base::.handleSimpleError(...)
25. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ensembldb.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'mean': database or disk is full
--- failed re-building ‘ensembldb.Rmd’
--- re-building ‘proteins.Rmd’ using rmarkdown
--- finished re-building ‘proteins.Rmd’
SUMMARY: processing the following file failed:
‘ensembldb.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
!pdfTeX error: pdflatex: fflush() failed (No space left on device)
==> Fatal error occurred, no output PDF file produced!
* checking PDF version of manual without index ... ERROR
* DONE
Status: 4 ERRORs, 3 WARNINGs, 1 NOTE
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ensembldb.Rcheck/00check.log’
for details.
ensembldb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL ensembldb ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘ensembldb’ ... ** this is package ‘ensembldb’ version ‘2.31.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘.cds_for_id2’ in package ‘ensembldb’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ensembldb)
ensembldb.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ensembldb)
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.
Loading required package: AnnotationFilter
Attaching package: 'AnnotationFilter'
The following object is masked from 'package:testthat':
not
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
> library(EnsDb.Hsapiens.v86)
> edb <- EnsDb.Hsapiens.v86
>
> test_check("ensembldb")
Comparing protein data:
[ FAIL 21 | WARN 117 | SKIP 3 | PASS 1295 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_Methods.R:129:1', 'test_Methods.R:273:1',
'test_seqLevelStyle.R:40:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_Methods.R:462:5'): lengthOf works ──────────────────────────────
Error: database or disk is full
Backtrace:
▆
1. └─ensembldb:::.transcriptLengths(...) at test_Methods.R:462:5
2. ├─GenomicFeatures::exonsBy(x, filter = TxIdFilter(allTxs$tx_id))
3. └─ensembldb::exonsBy(x, filter = TxIdFilter(allTxs$tx_id))
4. └─ensembldb (local) .local(x, by, ...)
5. ├─ensembldb:::getWhat(...)
6. └─ensembldb:::getWhat(...)
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::dbSendQuery(conn, statement, ...)
13. └─RSQLite::dbSendQuery(conn, statement, ...)
14. └─RSQLite (local) .local(conn, statement, ...)
15. ├─methods::new(...)
16. │ ├─methods::initialize(value, ...)
17. │ └─methods::initialize(value, ...)
18. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_Methods.R:837:5'): ordering works in genes calls ───────────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::genes(edb, return.type = "data.frame") at test_Methods.R:837:5
2. └─ensembldb::genes(edb, return.type = "data.frame")
3. └─ensembldb (local) .local(x, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_dbhelpers.R:390:9'): query is valid ────────────────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::transcripts(...) at test_dbhelpers.R:390:9
2. └─ensembldb::transcripts(...)
3. └─ensembldb (local) .local(x, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_functions-create-EnsDb.R:13:5'): ensDbFromGRanges works ────────
Error: database or disk is full
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_functions-create-EnsDb.R:13:5
2. │ └─base::withCallingHandlers(...)
3. └─ensembldb::ensDbFromGRanges(...)
4. └─ensembldb:::.createEnsDbIndices(con)
5. ├─DBI::dbExecute(...)
6. └─DBI::dbExecute(...)
7. ├─DBI::dbSendStatement(conn, statement, ...)
8. └─DBI::dbSendStatement(conn, statement, ...)
9. ├─DBI::dbSendQuery(conn, statement, ...)
10. └─RSQLite::dbSendQuery(conn, statement, ...)
11. └─RSQLite (local) .local(conn, statement, ...)
12. ├─methods::new(...)
13. │ ├─methods::initialize(value, ...)
14. │ └─methods::initialize(value, ...)
15. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_functions-create-EnsDb.R:39:5'): ensDbFromGtf and Gff works ────
Error: database or disk is full
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_functions-create-EnsDb.R:39:5
2. │ └─base::withCallingHandlers(...)
3. ├─ensembldb::EnsDb(ensDbFromGff(gff, outfile = tempfile(), skip = TRUE))
4. └─ensembldb::ensDbFromGff(gff, outfile = tempfile(), skip = TRUE)
5. └─ensembldb::ensDbFromGRanges(...)
6. ├─DBI::dbWriteTable(...)
7. └─RSQLite::dbWriteTable(...)
8. └─RSQLite (local) .local(conn, name, value, ...)
9. ├─DBI::dbCommit(conn, name = savepoint_id)
10. └─RSQLite::dbCommit(conn, name = savepoint_id)
11. └─RSQLite (local) .local(conn, ...)
12. ├─DBI::dbExecute(...)
13. └─DBI::dbExecute(...)
14. ├─DBI::dbSendStatement(conn, statement, ...)
15. └─DBI::dbSendStatement(conn, statement, ...)
16. ├─DBI::dbSendQuery(conn, statement, ...)
17. └─RSQLite::dbSendQuery(conn, statement, ...)
18. └─RSQLite (local) .local(conn, statement, ...)
19. ├─methods::new(...)
20. │ ├─methods::initialize(value, ...)
21. │ └─methods::initialize(value, ...)
22. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_functions-create-EnsDb.R:234:9'): getSeqlengthsFromMysqlFolder works ──
Error in `download.file(url = paste0(base_url, "/", file_name), destfile = tmp_file,
quiet = TRUE)`: cannot open URL 'ftp://ftp.ensembl.org/pub/release-86/mysql/homo_sapiens_core_86_38/seq_region.txt.gz'
Backtrace:
▆
1. └─ensembldb:::.getSeqlengthsFromMysqlFolder(...) at test_functions-create-EnsDb.R:234:9
2. └─ensembldb:::.getReadMysqlTable(...)
3. └─utils::download.file(...)
── Error ('test_genomeToX.R:100:5'): .genome_to_tx and genomeToTranscript works ──
Error: database or disk is full
Backtrace:
▆
1. └─ensembldb:::.genome_to_tx(gnm, edbx) at test_genomeToX.R:100:5
2. ├─GenomicFeatures::exonsBy(...)
3. └─ensembldb::exonsBy(...)
4. └─ensembldb (local) .local(x, by, ...)
5. ├─ensembldb:::getWhat(...)
6. └─ensembldb:::getWhat(...)
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::dbSendQuery(conn, statement, ...)
13. └─RSQLite::dbSendQuery(conn, statement, ...)
14. └─RSQLite (local) .local(conn, statement, ...)
15. ├─methods::new(...)
16. │ ├─methods::initialize(value, ...)
17. │ └─methods::initialize(value, ...)
18. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_genomeToX.R:257:5'): genomeToProtein works ─────────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─ProtGenerics::proteins(edb) at test_genomeToX.R:257:5
2. └─ensembldb::proteins(edb)
3. └─ensembldb (local) .local(object, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_proteinToGenome.R:92:5'): .cds_for_id and .cds_matching_protein work ──
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::cdsBy(...) at test_proteinToGenome.R:92:5
2. └─ensembldb::cdsBy(...)
3. └─ensembldb (local) .local(x, by, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_proteinToGenome.R:176:5'): proteinToGenome works ───────────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::cdsBy(...) at test_proteinToGenome.R:176:5
2. └─ensembldb::cdsBy(...)
3. └─ensembldb (local) .local(x, by, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_proteinToGenome.R:270:5'): proteinToTranscript works ───────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::cdsBy(...) at test_proteinToGenome.R:270:5
2. └─ensembldb::cdsBy(...)
3. └─ensembldb (local) .local(x, by, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_select-methods.R:151:5'): select method works ──────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─AnnotationDbi::select(edb, keys = GenenameFilter("NR3C1")) at test_select-methods.R:151:5
2. └─ensembldb::select(edb, keys = GenenameFilter("NR3C1"))
3. └─ensembldb:::.select(...)
4. ├─ensembldb:::getWhat(x, columns = ensCols, filter = keys, startWith = startWith)
5. └─ensembldb:::getWhat(x, columns = ensCols, filter = keys, startWith = startWith)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_select-methods.R:248:5'): mapIds works ─────────────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─AnnotationDbi::mapIds(...) at test_select-methods.R:248:5
2. └─ensembldb::mapIds(edb, keys = allgenes, keytype = "GENEID", column = "GENENAME")
3. └─ensembldb:::.mapIds(...)
4. ├─AnnotationDbi::select(x, keys = keys, columns = columns, keytype = keytype)
5. └─ensembldb::select(x, keys = keys, columns = columns, keytype = keytype)
6. └─ensembldb:::.select(...)
7. ├─ensembldb:::getWhat(x, columns = ensCols, filter = keys, startWith = startWith)
8. └─ensembldb:::getWhat(x, columns = ensCols, filter = keys, startWith = startWith)
9. └─ensembldb (local) .local(x, ...)
10. └─ensembldb:::.getWhat(...)
11. ├─DBI::dbGetQuery(dbconn(x), Q)
12. └─DBI::dbGetQuery(dbconn(x), Q)
13. └─DBI (local) .local(conn, statement, ...)
14. ├─DBI::dbFetch(rs, n = n, ...)
15. └─RSQLite::dbFetch(rs, n = n, ...)
16. └─RSQLite (local) .local(res, n, ...)
17. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_seqLevelStyle.R:107:5'): genes works with seqlevelsStyles ──────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::genes(edb) at test_seqLevelStyle.R:107:5
2. └─ensembldb::genes(edb)
3. └─ensembldb (local) .local(x, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_transcriptToX.R:89:5'): .tx_to_protein works ───────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─ProtGenerics::proteins(edbx) at test_transcriptToX.R:89:5
2. └─ensembldb::proteins(edbx)
3. └─ensembldb (local) .local(object, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_transcriptToX.R:117:5'): transcriptToProtein works ─────────────
Error: database or disk is full
Backtrace:
▆
1. ├─ProtGenerics::proteins(edbx) at test_transcriptToX.R:117:5
2. └─ensembldb::proteins(edbx)
3. └─ensembldb (local) .local(object, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_transcriptToX.R:174:5'): .tx_to_genome works ───────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::exonsBy(edbx) at test_transcriptToX.R:174:5
2. └─ensembldb::exonsBy(edbx)
3. └─ensembldb (local) .local(x, by, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbSendQuery(conn, statement, ...)
12. └─RSQLite::dbSendQuery(conn, statement, ...)
13. └─RSQLite (local) .local(conn, statement, ...)
14. ├─methods::new(...)
15. │ ├─methods::initialize(value, ...)
16. │ └─methods::initialize(value, ...)
17. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_transcriptToX.R:238:5'): transcriptToGenome works ──────────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::exonsBy(edbx) at test_transcriptToX.R:238:5
2. └─ensembldb::exonsBy(edbx)
3. └─ensembldb (local) .local(x, by, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbSendQuery(conn, statement, ...)
12. └─RSQLite::dbSendQuery(conn, statement, ...)
13. └─RSQLite (local) .local(conn, statement, ...)
14. ├─methods::new(...)
15. │ ├─methods::initialize(value, ...)
16. │ └─methods::initialize(value, ...)
17. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_transcriptToX.R:313:5'): transcriptToCds works ─────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::exonsBy(edb18) at test_transcriptToX.R:313:5
2. └─ensembldb::exonsBy(edb18)
3. └─ensembldb (local) .local(x, by, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbSendQuery(conn, statement, ...)
12. └─RSQLite::dbSendQuery(conn, statement, ...)
13. └─RSQLite (local) .local(conn, statement, ...)
14. ├─methods::new(...)
15. │ ├─methods::initialize(value, ...)
16. │ └─methods::initialize(value, ...)
17. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_transcriptToX.R:389:5'): cdsToTranscript works ─────────────────
Error: database or disk is full
Backtrace:
▆
1. ├─GenomicFeatures::exonsBy(EnsDb.Hsapiens.v86) at test_transcriptToX.R:389:5
2. └─ensembldb::exonsBy(EnsDb.Hsapiens.v86)
3. └─ensembldb (local) .local(x, by, ...)
4. ├─ensembldb:::getWhat(...)
5. └─ensembldb:::getWhat(...)
6. └─ensembldb (local) .local(x, ...)
7. └─ensembldb:::.getWhat(...)
8. ├─DBI::dbGetQuery(dbconn(x), Q)
9. └─DBI::dbGetQuery(dbconn(x), Q)
10. └─DBI (local) .local(conn, statement, ...)
11. ├─DBI::dbFetch(rs, n = n, ...)
12. └─RSQLite::dbFetch(rs, n = n, ...)
13. └─RSQLite (local) .local(res, n, ...)
14. └─RSQLite:::result_fetch(res@ptr, n = n)
── Error ('test_validity.R:16:9'): compareProteins works ───────────────────────
Error: database or disk is full
Backtrace:
▆
1. └─ensembldb:::compareProteins(edb, edb) at test_validity.R:16:9
2. ├─ProtGenerics::proteins(x)
3. └─ensembldb::proteins(x)
4. └─ensembldb (local) .local(object, ...)
5. ├─ensembldb:::getWhat(...)
6. └─ensembldb:::getWhat(...)
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 21 | WARN 117 | SKIP 3 | PASS 1295 ]
Error: Test failures
Execution halted
ensembldb.Rcheck/ensembldb-Ex.timings
| name | user | system | elapsed |